1
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Kuan KY, Hsu CP. Predicting Selectivity with a Bifurcating Surface: Inaccurate Model or Inaccurate Statistics of Dynamics? J Phys Chem A 2024; 128:6798-6805. [PMID: 39099446 PMCID: PMC11331512 DOI: 10.1021/acs.jpca.4c04039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024]
Abstract
Reactions on post-transition-state bifurcation (PTSB) energy surfaces are an important class of reaction in which classical rate theories, such as the transition state theory, fail to account for the selectivity. Quasiclassical trajectory molecular dynamic (QCT-MD) simulation is an important computational approach to understanding reactions mechanisms, especially for reactions that cannot be predicted from conventional rate theories. However, the applicability of direct dynamic simulations is hampered by huge computational costs for collecting a statistically meaningful set of trajectories, making it difficult to compare simulation results with theoretical or physical insights-based predictions (non-MD predictions). In this work, we examine the PTSB of Schmidt-Aubé reactions studied by Tantillo and co-workers. With machine-learning using kernel-ridge regression (KRR) to predict atomic forces, statistical reliability was enhanced by significantly increasing the number of trajectories. With KRR, the bottleneck of simulating dynamics (atomic forces in QCT-MD with density functional theory) was accelerated more than 100-fold. We found that this KRR-aided QCT-MD approach is successful in predicting branching ratios with a much larger number of trajectories. With our approach, statistical errors are greatly reduced, and hypothetical non-MD models for predicting selectivity are tested with much higher confidence. By comparison with non-MD models, dynamical properties that affect branching ratios become more clearly described.
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Affiliation(s)
- Kai-Yuan Kuan
- Institute
of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Chao-Ping Hsu
- Institute
of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
- Physics
Division, National Center for Theoretical
Sciences, 1, Section
4, Roosevelt Road, Taipei 106, Taiwan
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2
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Kadiyam RK, Sangolkar AA, Faizan M, Pawar R. Bispericyclic Ambimodal Dimerization of Pentafulvene: The Origin of Asynchronicity and Kinetic Selectivity of the Endo Transition State. J Org Chem 2024; 89:6813-6825. [PMID: 38661667 DOI: 10.1021/acs.joc.4c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The propensity of fulvenes to undergo dimerization has long been known, although the in-depth mechanism and electronic behavior during dimerization are still elusive. Herein, we made an attempt to gain insights into the reactivity of pentafulvene for Diels-Alder (DA) and [6 + 4]-cycloadditions via conventional and ambimodal routes. The result emphasizes that pentafulvene dimerization preferentially proceeds through a unique bifurcation mechanism where two DA pathways merge together to produce two degenerate [4 + 2]-cycloadducts from a single TS. Despite the [6 + 4]-cycloadduct being thermodynamically preferred, [4 + 2]-cycloaddition reactions are kinetically driven. Singlet biradicaloid is involved in through-space 6e- delocalization as a secondary orbital interaction that originates asynchronicity and stabilizes the bispericyclic transition state (TS). The transformation of various actively participating intrinsic bonding orbitals (IBOs) unambiguously forecasts the formation of multiple products from a single TS and rationalizes the mechanism of ambimodal reactions that are rather difficult to probe with other analyses. The changes in active IBOs clearly distinguish the conventional reactions from bifurcation reactions and can be employed to characterize and confirm the ambimodal mechanism. This report gains a crucial theoretical insight into the mechanism of bifurcation, the origin of asynchronicity, and electronic behavior in ambimodal TS, which will certainly be of enormous value for future studies.
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Affiliation(s)
- Rama Krishna Kadiyam
- Laboratory of Advanced Computation and Theory for Materials and Chemistry, Department of Chemistry, National Institute of Technology Warangal (NITW), Warangal, Telangana 506004, India
| | - Akanksha Ashok Sangolkar
- Laboratory of Advanced Computation and Theory for Materials and Chemistry, Department of Chemistry, National Institute of Technology Warangal (NITW), Warangal, Telangana 506004, India
| | - Mohmmad Faizan
- Laboratory of Advanced Computation and Theory for Materials and Chemistry, Department of Chemistry, National Institute of Technology Warangal (NITW), Warangal, Telangana 506004, India
| | - Ravinder Pawar
- Laboratory of Advanced Computation and Theory for Materials and Chemistry, Department of Chemistry, National Institute of Technology Warangal (NITW), Warangal, Telangana 506004, India
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3
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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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4
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Loco D, Chataigner I, Piquemal J, Spezia R. Efficient and Accurate Description of Diels-Alder Reactions Using Density Functional Theory. Chemphyschem 2022; 23:e202200349. [PMID: 35696652 PMCID: PMC9796631 DOI: 10.1002/cphc.202200349] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/11/2022] [Indexed: 01/01/2023]
Abstract
Modeling chemical reactions using Quantum Chemistry is a widely used predictive strategy capable to complement experiments in order to understand the intrinsic mechanisms guiding the chemicals towards the most favorable reaction products. However, at this purpose, it is mandatory to use reliable and computationally tractable theoretical methods. In this work, we focus on six Diels-Alder reactions of increasing complexity and perform an extensive benchmark of middle- to low-cost computational approaches to predict the characteristic reactions energy barriers. We found that Density Functional Theory, using the ωB97XD, LC-ωPBE, CAM-B3LYP, M11 and MN12SX functionals, with empirical dispersion corrections coupled to an affordable 6-31G basis set, provides quality results for this class of reactions, at a small computational effort. Such efficient and reliable simulation protocol opens perspectives for hybrid QM/MM molecular dynamics simulations of Diels-Alder reactions including explicit solvation.
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Affiliation(s)
- Daniele Loco
- Sorbonne Université, Laboratoire de Chimie ThéoriqueUMR 7616 CNRS4 Place Jussieu75005ParisFrance
- Qubit PharmaceuticalsIncubateur Paris Biotech Santé24 rue du Faubourg Saint Jacques75014ParisFrance
| | - Isabelle Chataigner
- Sorbonne Université, Laboratoire de Chimie ThéoriqueUMR 7616 CNRS4 Place Jussieu75005ParisFrance
- Normandie Univ.UNIROUENCNRS, INSA Rouen, COBRA76000RouenFrance
| | - Jean‐Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie ThéoriqueUMR 7616 CNRS4 Place Jussieu75005ParisFrance
| | - Riccardo Spezia
- Sorbonne Université, Laboratoire de Chimie ThéoriqueUMR 7616 CNRS4 Place Jussieu75005ParisFrance
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5
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Melville J, Hargis C, Davenport MT, Hamilton RS, Ess DH. Machine Learning Analysis of Dynamic‐Dependent Bond Formation in Trajectories with Consecutive Transition States. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jesse Melville
- Department of Chemistry and Biochemistry Brigham Young University Provo Utah USA
| | - Cal Hargis
- Department of Chemistry and Biochemistry Brigham Young University Provo Utah USA
| | - Michael T. Davenport
- Department of Chemistry and Biochemistry Brigham Young University Provo Utah USA
| | - R. Spencer Hamilton
- Department of Chemistry and Biochemistry Brigham Young University Provo Utah USA
| | - Daniel H. Ess
- Department of Chemistry and Biochemistry Brigham Young University Provo Utah USA
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6
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Ito T, Maeda S, Harabuchi Y. Kinetic Analysis of a Reaction Path Network Including Ambimodal Transition States: A Case Study of an Intramolecular Diels-Alder Reaction. J Chem Theory Comput 2022; 18:1663-1671. [PMID: 35099971 DOI: 10.1021/acs.jctc.1c01297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study proposes a methodology for the kinetic analysis of a reaction path network including ambimodal transition states (TSs), through which an ensemble of trajectories bifurcates to multiple minima in a phenomenon called dynamical bifurcation. The proposed methodology consists of three techniques: an automated reaction path search to construct a reaction path network including ambimodal TSs, an ab initio molecular dynamics simulation to evaluate the branching ratio, and the definition of rate constants incorporating this ratio. Applying the procedure to a Diels-Alder reaction, it was found that the inclusion of dynamical bifurcations is necessary to explain the experimental reaction yield of a byproduct. In addition, it was verified that the products take 1013 s to reach thermal equilibrium and that the experimental selectivity is determined by the dynamical bifurcations.
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Affiliation(s)
- Takuma Ito
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan.,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO) Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Sapporo 060-0810, Japan
| | - Yu Harabuchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan.,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO) Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Sapporo 060-0810, Japan
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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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Dale HJA, Leach AG, Lloyd-Jones GC. Heavy-Atom Kinetic Isotope Effects: Primary Interest or Zero Point? J Am Chem Soc 2021; 143:21079-21099. [PMID: 34870970 DOI: 10.1021/jacs.1c07351] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chemists have many options for elucidating reaction mechanisms. Global kinetic analysis and classic transition-state probes (e.g., LFERs, Eyring) inevitably form the cornerstone of any strategy, yet their application to increasingly sophisticated synthetic methodologies often leads to a wide range of indistinguishable mechanistic proposals. Computational chemistry provides powerful tools for narrowing the field in such cases, yet wholly simulated mechanisms must be interpreted with great caution. Heavy-atom kinetic isotope effects (KIEs) offer an exquisite but underutilized method for reconciling the two approaches, anchoring the theoretician in the world of calculable observables and providing the experimentalist with atomistic insights. This Perspective provides a personal outlook on this synergy. It surveys the computation of heavy-atom KIEs and their measurement by NMR spectroscopy, discusses recent case studies, highlights the intellectual reward that lies in alignment of experiment and theory, and reflects on the changes required in chemical education in the area.
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Affiliation(s)
- Harvey J A Dale
- EaStChem, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Andrew G Leach
- School of Health Sciences, The University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, U.K
| | - Guy C Lloyd-Jones
- EaStChem, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
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9
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Qin ZX, Tremblay M, Hong X, Yang ZJ. Entropic Path Sampling: Computational Protocol to Evaluate Entropic Profile along a Reaction Path. J Phys Chem Lett 2021; 12:10713-10719. [PMID: 34709848 DOI: 10.1021/acs.jpclett.1c03116] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fleeting intermediates constitute dynamically stepwise mechanisms. They have been characterized in molecular dynamics trajectories, but whether these intermediates form a free energy minimum to become entropic intermediates remains elusively defined. We developed a computational protocol known as entropic path sampling to evaluate the entropic variation of reacting species along a reaction path based on an ensemble of trajectories. Using cyclopentadiene dimerization as a model reaction, we observed an entropy maximum along the reaction path which originates from an enhanced conformational flexibility as the reacting species enter into a flat energy region. As the reacting species further approach product formation, unfavorable entropic restriction fails to offset the potential energy drop, resulting in no free energy minimum along the post-TS pathway. Our results show that cyclopentadiene dimerization involves an entropy maximum that leads to dynamic intermediates with elongated lifetimes, but the reaction does not involve entropic intermediates.
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Affiliation(s)
- Zhi-Xin Qin
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, China
| | - Matthew Tremblay
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Xin Hong
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, China
| | - 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
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
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10
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Liu Y, Holm S, Meisner J, Jia Y, Wu Q, Woods TJ, Martinez TJ, Moore JS. Flyby reaction trajectories: Chemical dynamics under extrinsic force. Science 2021; 373:208-212. [PMID: 34244412 DOI: 10.1126/science.abi7609] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/03/2021] [Indexed: 11/02/2022]
Abstract
Dynamic effects are an important determinant of chemical reactivity and selectivity, but the deliberate manipulation of atomic motions during a chemical transformation is not straightforward. Here, we demonstrate that extrinsic force exerted upon cyclobutanes by stretching pendant polymer chains influences product selectivity through force-imparted nonstatistical dynamic effects on the stepwise ring-opening reaction. The high product stereoselectivity is quantified by carbon-13 labeling and shown to depend on external force, reactant stereochemistry, and intermediate stability. Computational modeling and simulations show that, besides altering energy barriers, the mechanical force activates reactive intramolecular motions nonstatistically, setting up "flyby trajectories" that advance directly to product without isomerization excursions. A mechanistic model incorporating nonstatistical dynamic effects accounts for isomer-dependent mechanochemical stereoselectivity.
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Affiliation(s)
- Yun Liu
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Soren Holm
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,The PULSE Institute, Stanford University, Stanford, CA 94305, USA.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jan Meisner
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,The PULSE Institute, Stanford University, Stanford, CA 94305, USA.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Yuan Jia
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Qiong Wu
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Toby J Woods
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,3M Materials Chemistry Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Todd J Martinez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA. .,The PULSE Institute, Stanford University, Stanford, CA 94305, USA.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jeffrey S Moore
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. .,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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11
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Li B, Li Y, Dang Y, Houk KN. Post-Transition State Bifurcation in Iron-Catalyzed Arene Aminations. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Bo Li
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, School of Science, Tianjin University, Tianjin 300072, China
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Yuli Li
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, School of Science, Tianjin University, Tianjin 300072, China
| | - Yanfeng Dang
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, School of Science, Tianjin University, Tianjin 300072, China
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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12
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Jiang H, Tao X, Kammler M, Ding F, Wodtke AM, Kandratsenka A, Miller TF, Bünermann O. Small Nuclear Quantum Effects in Scattering of H and D from Graphene. J Phys Chem Lett 2021; 12:1991-1996. [PMID: 33596383 DOI: 10.1021/acs.jpclett.0c02933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We study nuclear quantum effects in H/D sticking to graphene, comparing scattering experiments at near-zero coverage with classical, quantized, and transition-state calculations. The experiment shows H/D sticking probabilities that are indistinguishable from one another and markedly smaller than those expected from a consideration of zero-point energy shifts of the chemisorption transition state. Inclusion of dynamical effects and vibrational anharmonicity via ring-polymer molecular dynamics (RPMD) yields results that are in good agreement with the experimental results. RPMD also reveals that nuclear quantum effects, while modest, arise primarily from carbon and not from H/D motion, confirming the importance of a C atom rehybridization mechanism associated with H/D sticking on graphene.
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Affiliation(s)
- Hongyan Jiang
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
| | - Xuecheng Tao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Marvin Kammler
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
| | - Feizhi Ding
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Alec M Wodtke
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
- Institut für Physikalische Chemie, Georg-Georg-August-Universität Göttingen, Tammanstraße 6, 37077 Göttingen, Germany
- International Center for Advanced Studies of Energy Conversion, Georg-August University of Göttingen, Tammanstraße 6, 37077 Göttingen, Germany
| | - Alexander Kandratsenka
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Oliver Bünermann
- Department of Dynamics at Surfaces, Max-Planck-Institute for Biophysical Chemistry, Am Faßerg 11, 37077 Göttingen, Germany
- Institut für Physikalische Chemie, Georg-Georg-August-Universität Göttingen, Tammanstraße 6, 37077 Göttingen, Germany
- International Center for Advanced Studies of Energy Conversion, Georg-August University of Göttingen, Tammanstraße 6, 37077 Göttingen, Germany
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13
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Houk KN, Liu F, Yang Z, Seeman JI. Die Evolution des Diels‐Alder‐Reaktionsmechanismus seit den 1930er Jahren: Woodward, Houk zusammen mit Woodward und der Einfluss der Computerchemie auf das Verständnis von Cycloadditionen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202001654] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Kendall N. Houk
- Department of Chemistry and Biochemistry University of California Los Angeles California 90005 USA
| | - Fang Liu
- Department of Chemistry and Biochemistry University of California Los Angeles California 90005 USA
- College of Sciences Nanjing Agricultural University Nanjing 210095 China
| | - Zhongyue Yang
- Department of Chemistry and Biochemistry University of California Los Angeles California 90005 USA
| | - Jeffrey I. Seeman
- Department of Chemistry University of Richmond Richmond Virginia 23173 USA
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14
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Houk KN, Liu F, Yang Z, Seeman JI. Evolution of the Diels–Alder Reaction Mechanism since the 1930s: Woodward, Houk with Woodward, and the Influence of Computational Chemistry on Understanding Cycloadditions. Angew Chem Int Ed Engl 2021; 60:12660-12681. [DOI: 10.1002/anie.202001654] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/30/2020] [Indexed: 01/16/2023]
Affiliation(s)
- Kendall N. Houk
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90005 USA
| | - Fang Liu
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90005 USA
- College of Sciences Nanjing Agricultural University Nanjing 210095 China
| | - Zhongyue Yang
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90005 USA
| | - Jeffrey I. Seeman
- Department of Chemistry University of Richmond Richmond VA 23173 USA
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15
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Roytman VA, Singleton DA. Solvation Dynamics and the Nature of Reaction Barriers and Ion-Pair Intermediates in Carbocation Reactions. J Am Chem Soc 2020; 142:12865-12877. [DOI: 10.1021/jacs.0c06295] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Vladislav A. Roytman
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
| | - Daniel A. Singleton
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
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16
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Yang Y, Zhang X, Zhong LP, Lan J, Li X, Li CC, Chung LW. Unusual KIE and dynamics effects in the Fe-catalyzed hetero-Diels-Alder reaction of unactivated aldehydes and dienes. Nat Commun 2020; 11:1850. [PMID: 32296076 PMCID: PMC7160212 DOI: 10.1038/s41467-020-15599-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/13/2020] [Indexed: 12/30/2022] Open
Abstract
Hetero-Diels-Alder (HDA) reaction is an important synthetic method for many natural products. An iron(III) catalyst was developed to catalyze the challenging HDA reaction of unactivated aldehydes and dienes with high selectivity. Here we report extensive density-functional theory (DFT) calculations and molecular dynamics simulations that show effects of iron (including its coordinate mode and/or spin state) on the dynamics of this reaction: considerably enhancing dynamically stepwise process, broadening entrance channel and narrowing exit channel from concerted asynchronous transition states. Also, our combined computational and experimental secondary KIE studies reveal unexpectedly large KIE values for the five-coordinate pathway even with considerable C-C bond forming, due to equilibrium isotope effect from the change in the metal coordination. Moreover, steric and electronic effects are computationally shown to dictate the C=O chemoselectivity for an α,β-unsaturated aldehyde, which is verified experimentally. Our mechanistic study may help design homogeneous, heterogeneous and biological catalysts for this challenging reaction.
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Affiliation(s)
- Yuhong Yang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiaoyong Zhang
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Li-Ping Zhong
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jialing Lan
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xin Li
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chuang-Chuang Li
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.
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17
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Ito T, Harabuchi Y, Maeda S. AFIR explorations of transition states of extended unsaturated systems: automatic location of ambimodal transition states. Phys Chem Chem Phys 2020; 22:13942-13950. [DOI: 10.1039/d0cp02379e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on the artificial force induced reaction (AFIR) method, we proposed a procedure to systematically explore ambimodal transition states (TSs) that cause the dynamical bifurcation.
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Affiliation(s)
- Takuma Ito
- Graduate School of Chemical Sciences and Engineering
- Hokkaido University
- Sapporo 060-8628
- Japan
| | - Yu Harabuchi
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
| | - Satoshi Maeda
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
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18
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Roytman VA, Jin S, Nguyen VT, Nguyen VD, Haug GC, Larionov OV, Singleton DA. Bond Memory in Dynamically Determined Stereoselectivity. J Am Chem Soc 2019; 142:85-88. [PMID: 31852185 DOI: 10.1021/jacs.9b12227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The carboborative ring contraction of cyclohexenes exhibits an abnormal selectivity pattern in which a formally concerted double migration gives rise to predominant but not exclusive inversion products. In dynamic trajectories, the inversion and retention products are formed from the same transition state, and the trajectories accurately account for the experimental product ratios. The unusual origin of the selectivity is the dynamically retained non-equivalence of newly formed versus pre-existing bonds after the first bond migration.
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Affiliation(s)
- Vladislav A Roytman
- Department of Chemistry , Texas A&M University , P.O. Box 30012, College Station , Texas 77842 , United States
| | - Shengfei Jin
- Department of Chemistry , The University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Vu T Nguyen
- Department of Chemistry , The University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Viet D Nguyen
- Department of Chemistry , The University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Graham C Haug
- Department of Chemistry , The University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Oleg V Larionov
- Department of Chemistry , The University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Daniel A Singleton
- Department of Chemistry , Texas A&M University , P.O. Box 30012, College Station , Texas 77842 , United States
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19
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Qin XJ, Rauwolf TJ, Li PP, Liu H, McNeely J, Hua Y, Liu HY, Porco JA. Isolation and Synthesis of Novel Meroterpenoids from Rhodomyrtus tomentosa: Investigation of a Reactive Enetrione Intermediate. Angew Chem Int Ed Engl 2019; 58:4291-4296. [PMID: 30681258 PMCID: PMC6583783 DOI: 10.1002/anie.201814421] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Indexed: 01/19/2023]
Abstract
Rhodomyrtusials A-C, the first examples of triketone-sesquiterpene meroterpenoids featuring a unique 6/5/5/9/4 fused pentacyclic ring system were isolated from Rhodomyrtus tomentosa, along with several biogenetically-related dihydropyran isomers. Two bis-furans and one dihydropyran isomer showed acetylcholinesterase (AChE) inhibitory activity. Structures of the isolates were unambiguously established by a combination of spectroscopic data, ECD analysis, and total synthesis. Bioinspired total syntheses of six isolates were achieved in six steps utilizing a reactive enetrione intermediate generated in situ from a readily available hydroxy-endoperoxide precursor.
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Affiliation(s)
- Xu-Jie Qin
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences Kunming 650201 (P. R. China)
| | - Tyler J. Rauwolf
- Department of Chemistry, Center for Molecular Discovery (BUCMD), Boston University 590 Commonwealth Avenue, Boston, MA 02215 (USA)
| | - Pan-Pan Li
- College of Forestry, Southwest Forestry University Kunming 650224 (P. R. China)
| | - Hui Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences Kunming 650201 (P. R. China)
| | - James McNeely
- Department of Chemistry, Center for Molecular Discovery (BUCMD), Boston University 590 Commonwealth Avenue, Boston, MA 02215 (USA)
| | - Yan Hua
- College of Forestry, Southwest Forestry University Kunming 650224 (P. R. China)
| | - Hai-Yang Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences Kunming 650201 (P. R. China)
| | - John A. Porco
- Department of Chemistry, Center for Molecular Discovery (BUCMD), Boston University 590 Commonwealth Avenue, Boston, MA 02215 (USA)
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20
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Qin X, Rauwolf TJ, Li P, Liu H, McNeely J, Hua Y, Liu H, Porco JA. Isolation and Synthesis of Novel Meroterpenoids from
Rhodomyrtus tomentos
a: Investigation of a Reactive Enetrione Intermediate. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814421] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xu‐Jie Qin
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 P. R. China
| | - Tyler J. Rauwolf
- Department of Chemistry Center for Molecular Discovery (BU-CMD) Boston University 590 Commonwealth Avenue Boston MA 02215 USA
| | - Pan‐Pan Li
- College of Forestry Southwest Forestry University Kunming 650224 P. R. China
| | - Hui Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 P. R. China
| | - James McNeely
- Department of Chemistry Center for Molecular Discovery (BU-CMD) Boston University 590 Commonwealth Avenue Boston MA 02215 USA
| | - Yan Hua
- College of Forestry Southwest Forestry University Kunming 650224 P. R. China
| | - Hai‐Yang Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 P. R. China
| | - John A. Porco
- Department of Chemistry Center for Molecular Discovery (BU-CMD) Boston University 590 Commonwealth Avenue Boston MA 02215 USA
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21
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Burns JM, Boittier ED. Pathway Bifurcation in the (4 + 3)/(5 + 2)-Cycloaddition of Butadiene and Oxidopyrylium Ylides: The Significance of Molecular Orbital Isosymmetry. J Org Chem 2019; 84:5997-6005. [DOI: 10.1021/acs.joc.8b03236] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jed M. Burns
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4067 Queensland, Australia
| | - Eric D. Boittier
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4067 Queensland, Australia
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22
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Yu Y, Yang Z, Houk KN. Molecular dynamics of the intramolecular 1, 3-dipolar ene reaction of a nitrile oxide and an alkene: non-statistical behavior of a reaction involving a diradical intermediate. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1549338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Yanmin Yu
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, Beijing University of Technology, Beijing, People’s Republic of China
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Zhongyue Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
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23
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Molecular dynamics of the two-stage mechanism of cyclopentadiene dimerization: concerted or stepwise? Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.02.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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24
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Yang Z, Houk KN. The Dynamics of Chemical Reactions: Atomistic Visualizations of Organic Reactions, and Homage to van ’t Hoff. Chemistry 2018. [DOI: 10.1002/chem.201706032] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Zhongyue Yang
- Department of Chemistry and Biochemistry; University of California; Los Angeles California 90095 USA
| | - K. N. Houk
- Department of Chemistry and Biochemistry; University of California; Los Angeles California 90095 USA
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25
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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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26
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Mandal N, Datta A. Dynamical Effects along the Bifurcation Pathway Control Semibullvalene Formation in Deazetization Reactions. J Phys Chem B 2018; 122:1239-1244. [PMID: 29316395 DOI: 10.1021/acs.jpcb.7b09533] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Post-transition-state dynamics during the deazetization of 3 resulting in two degenerate semibullvalenes (4 and 5) have been investigated with density functional theory (DFT) and quasi-classical trajectory (QCT) calculations. Removal of N2 from 3 occurs through a synchronous and concerted pathway through an ambimodal transition-state (TS1). In addition to TS2, the exclusively anticipated product from minimum energy pathway (MEP) calculations, trajectories initiated from TS1 produce 4, TS2, and 5 in 1:1:1 ratio. Isotopic substitutions (12C(13C/14C)-H(D) at 1-2 positions) result in purely Newtonian kinetic isotope effects (4:5 ≈ 1.4 for 13C1-13C2), an unequivocal evidence for dynamics controlled product formation.
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Affiliation(s)
- Nilangshu Mandal
- Department of Spectroscopy, Indian Association for the Cultivation of Science , 2A and 2B Raja S.C. Mallick Road, Kolkata 700032, India
| | - Ayan Datta
- Department of Spectroscopy, Indian Association for the Cultivation of Science , 2A and 2B Raja S.C. Mallick Road, Kolkata 700032, India
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27
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Burns JM. Computational evidence for a reaction pathway bifurcation in Sasaki-type (4 + 3)-cycloadditions. Org Biomol Chem 2018; 16:1828-1836. [DOI: 10.1039/c8ob00075a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Evidence for a post-transition state bifurcation in a (4 + 3)-cycloaddition is presented.
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Affiliation(s)
- Jed M. Burns
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
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28
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Li X, Liao T, Chung LW. Computational Prediction of Excited-State Carbon Tunneling in the Two Steps of Triplet Zimmerman Di-π-Methane Rearrangement. J Am Chem Soc 2017; 139:16438-16441. [PMID: 29037035 DOI: 10.1021/jacs.7b07539] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photoinduced Zimmerman di-π-methane (DPM) rearrangement of polycyclic molecules to form synthetically useful cyclopropane derivatives was found experimentally to proceed in a triplet excited state. We have applied state-of-the-art quantum mechanical methods, including M06-2X, DLPNO-CCSD(T) and variational transition-state theory with multidimensional tunneling corrections, to an investigation of the reaction rates of the two steps in the triplet DPM rearrangement of dibenzobarrelene, benzobarrelene and barrelene. This study predicts a high probability of carbon tunneling in regions around the two consecutive transition states at 200-300 K, and an enhancement in the rates by 104-276/35-67% with carbon tunneling at 200/300 K. The Arrhenius plots of the rate constants were found to be curved at low temperatures. Moreover, the computed 12C/13C kinetic isotope effects were affected significantly by carbon tunneling and temperature. Our predictions of electronically excited-state carbon tunneling and two consecutive carbon tunneling are unprecedented. Heavy-atom tunneling in some photoinduced reactions with reactive intermediates and narrow barriers can be potentially observed at relatively low temperature in experiments.
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Affiliation(s)
- Xin Li
- Department of Chemistry, South University of Science and Technology of China , Shenzhen 518055, China
| | - Tao Liao
- Department of Chemistry, South University of Science and Technology of China , Shenzhen 518055, China
| | - Lung Wa Chung
- Department of Chemistry, South University of Science and Technology of China , Shenzhen 518055, China
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29
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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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30
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Nieves-Quinones Y, Singleton DA. Dynamics and the Regiochemistry of Nitration of Toluene. J Am Chem Soc 2016; 138:15167-15176. [PMID: 27794598 DOI: 10.1021/jacs.6b07328] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The regiochemistry of the nitration of toluene by NO2+BF4- in dichloromethane is accurately predicted from trajectories in explicit solvent. Simpler models and approaches based on transition state theory fail to account for the selectivity. Potential of mean force calculations find no free-energy barrier for reaction of the toluene/NO2+BF4- encounter complex, yet the trajectories require an extraordinary 3 ps to descend an exergonic slope. The selectivity is decided late in long trajectories because their completion requires solvent and counterion reorganization. The normal descriptive understanding of the regiochemistry based on transition-state energies is unsupported.
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Affiliation(s)
- Yexenia Nieves-Quinones
- Department of Chemistry, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
| | - Daniel A Singleton
- Department of Chemistry, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
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31
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Doubleday C, Boguslav M, Howell C, Korotkin SD, Shaked D. Trajectory Calculations for Bergman Cyclization Predict H/D Kinetic Isotope Effects Due to Nonstatistical Dynamics in the Product. J Am Chem Soc 2016; 138:7476-9. [PMID: 27281683 DOI: 10.1021/jacs.6b03466] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An unusual H/D kinetic isotope effect (KIE) is described, in which isotopic selectivity arises primarily from nonstatistical dynamics in the product. In DFT-based quasiclassical trajectories of Bergman cyclization of (Z)-3-hexen-1,5-diyne (1) at 470 K, the new CC bond retains its energy, and 28% of nascent p-benzyne recrosses back to the enediyne on a vibrational time scale. The competing process of intramolecular vibrational redistribution (IVR) in p-benzyne is too slow to prevent this. Deuteration increases the rate of IVR, which decreases the fraction of recrossing and increases the yield of statistical (trapable) p-benzyne, 2. Trapable yields for three isotopomers of 2 range from 72% to 86%. The resulting KIEs for Bergman cyclization differ substantially from KIEs predicted by transition state theory, which suggests that IVR in this reaction can be studied by conventional KIEs. Leakage of vibrational zero point energy (ZPE) into the reaction coordinate was probed by trajectories in which initial ZPE in the CH/CD stretching modes was reduced by 25%. This did not change the predicted KIEs.
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Affiliation(s)
- Charles Doubleday
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
| | - Mayla Boguslav
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
| | - Caronae Howell
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
| | - Scott D Korotkin
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
| | - David Shaked
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
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32
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Abstract
![]()
Consideration
of the role of dynamic trajectories in [1,2]- and [2,3]-sigmatropic
rearrangements suggests a counterintuitive approach to controlling
the selectivity. In our hypothesis, [2,3] selectivity can be promoted
by reaction conditions that thermodynamically disfavor the [2,3] rearrangement
step and thereby make the transition state later. The application
of this idea has led to a successful prescription for dictating the
selectivity in Stevens/Sommelet-Hauser rearrangements of ammonium
ylides. A combination of kinetic isotope effects, crossover experiments,
and computational dynamic trajectories support the idea that the selectivity
is controlled through control of the path of trajectories.
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Affiliation(s)
- Bibaswan Biswas
- Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States
| | - Daniel A Singleton
- Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States
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33
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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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34
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Pu M, Privalov T. Chemistry of Intermolecular Frustrated Lewis Pairs in Motion: Emerging Perspectives and Prospects. Isr J Chem 2015. [DOI: 10.1002/ijch.201400159] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Carpenter BK, Harvey JN, Glowacki DR. Prediction of enhanced solvent-induced enantioselectivity for a ring opening with a bifurcating reaction path. Phys Chem Chem Phys 2015; 17:8372-81. [DOI: 10.1039/c4cp05078a] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fully atomistic molecular dynamics simulation predicts enhance induction of enantiomeric excess in the products of a reaction with a bifurcating reaction coordinate, when run in a chiral solvent.
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Affiliation(s)
| | | | - David R. Glowacki
- School of Chemistry
- University of Bristol
- Bristol
- UK
- Department of Computer Science
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36
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Alabugin IV, Bresch S, dos Passos Gomes G. Orbital hybridization: a key electronic factor in control of structure and reactivity. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3382] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Igor V. Alabugin
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
| | - Stefan Bresch
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
| | - Gabriel dos Passos Gomes
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
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37
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Alabugin IV, Bresch S, Manoharan M. Hybridization trends for main group elements and expanding the Bent's rule beyond carbon: more than electronegativity. J Phys Chem A 2014; 118:3663-77. [PMID: 24773162 DOI: 10.1021/jp502472u] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Trends in hybridization were systematically analyzed through the combination of DFT calculations with NBO analysis for the five elements X (X = B, C, N, O, and F) in 75 HnX-YHm compounds, where Y spans the groups 13-17 of the periods 2-4. This set of substrates probes the flexibility of the hybridization at five atoms X through variations in electronegativity, polarizability, and orbital size of Y. The results illustrate the scope and limitations of the Bent's rule, the classic correlation between electronegativity and hybridization, commonly used in analyzing structural effects in carbon compounds. The rehybridization effects are larger for fluorine- and oxygen-bonds than they are in the similar bonds to carbon. For bonds with the larger elements Y of the lower periods, trends in orbital hybridization depend strongly on both electronegativity and orbital size. For charged species, the effects of substituent orbital size in the more polarizable bonds to heavier elements show a particularly strong response to the charge introduction at the central atom. In the final section, we provide an example of the interplay between hybridization effects with molecular structure and reactivity. In particular, the ability to change hybridization without changes in polarization provides an alternative way to control structure and reactivity, as illustrated by the strong correlation of strain in monosubstituted cyclopropanes with hybridization in the bond to the substituent.
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Affiliation(s)
- Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306-4390, United States
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38
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Hong YJ, Tantillo DJ. Biosynthetic consequences of multiple sequential post-transition-state bifurcations. Nat Chem 2014; 6:104-11. [PMID: 24451585 DOI: 10.1038/nchem.1843] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 12/05/2013] [Indexed: 11/09/2022]
Abstract
Selectivity in chemical reactions that form complex molecular architectures from simpler precursors is usually rationalized by comparing competing transition-state structures that lead to different possible products. Herein we describe a system for which a single transition-state structure leads to the formation of many isomeric products via pathways that feature multiple sequential bifurcations. The reaction network described connects the pimar-15-en-8-yl cation to miltiradiene, a tricyclic diterpene natural product, and isomers via cyclizations and/or rearrangements. The results suggest that the selectivity of the reaction is controlled by (post-transition-state) dynamic effects, that is, how the carbocation structure changes in response to the distribution of energy in its vibrational modes. The inherent dynamical effects revealed herein (characterized through quasiclassical direct dynamics calculations using density functional theory) have implications not only for the general principles of selectivity prediction in systems with complex potential energy surfaces, but also for the mechanisms of terpene synthase enzymes and their evolution. These findings redefine the challenges faced by nature in controlling the biosynthesis of complex natural products.
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Affiliation(s)
- Young Joo Hong
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
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39
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Roston D, Islam Z, Kohen A. Isotope effects as probes for enzyme catalyzed hydrogen-transfer reactions. Molecules 2013; 18:5543-67. [PMID: 23673528 PMCID: PMC4342783 DOI: 10.3390/molecules18055543] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 04/30/2013] [Accepted: 05/03/2013] [Indexed: 11/16/2022] Open
Abstract
Kinetic Isotope effects (KIEs) have long served as a probe for the mechanisms of both enzymatic and solution reactions. Here, we discuss various models for the physical sources of KIEs, how experimentalists can use those models to interpret their data, and how the focus of traditional models has grown to a model that includes motion of the enzyme and quantum mechanical nuclear tunneling. We then present two case studies of enzymes, thymidylate synthase and alcohol dehydrogenase, and discuss how KIEs have shed light on the C-H bond cleavages those enzymes catalyze. We will show how the combination of both experimental and computational studies has changed our notion of how these enzymes exert their catalytic powers.
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Affiliation(s)
| | | | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
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40
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Manning KA, Sathyamoorthy B, Eletsky A, Szyperski T, Murkin AS. Highly precise measurement of kinetic isotope effects using 1H-detected 2D [13C,1H]-HSQC NMR spectroscopy. J Am Chem Soc 2012; 134:20589-92. [PMID: 23215000 DOI: 10.1021/ja310353c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new method is presented for measuring kinetic isotope effects (KIEs) by (1)H-detected 2D [(13)C,(1)H]-heteronuclear single quantum coherence (HSQC) NMR spectroscopy. The high accuracy of this approach was exemplified for the reaction catalyzed by glucose-6-phosphate dehydrogenase by comparing the 1-(13)C KIE with the published value obtained using isotope ratio mass spectrometry. High precision was demonstrated for the reaction catalyzed by 1-deoxy-D-xylulose-5-phosphate reductoisomerase from Mycobacterium tuberculosis. 2-, 3-, and 4-(13)C KIEs were found to be 1.0031(4), 1.0303(12), and 1.0148(2), respectively. These KIEs provide evidence for a cleanly rate-limiting retroaldol step during isomerization. The high intrinsic sensitivity and signal dispersion of 2D [(13)C,(1)H]-HSQC offer new avenues to study challenging systems where low substrate concentration and/or signal overlap impedes 1D (13)C NMR data acquisition. Moreover, this approach can take advantage of highest-field spectrometers, which are commonly equipped for (1)H detection with cryogenic probes.
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Affiliation(s)
- Kathryn A Manning
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, USA
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41
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Ion desolvation as a mechanism for kinetic isotope fractionation in aqueous systems. Proc Natl Acad Sci U S A 2012; 109:18689-94. [PMID: 23112160 DOI: 10.1073/pnas.1208184109] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics simulations show that the desolvation rates of isotopes of Li(+), K(+), Rb(+), Ca(2+), Sr(2+), and Ba(2+) may have a relatively strong dependence on the metal cation mass. This inference is based on the observation that the exchange rate constant, k(wex), for water molecules in the first hydration shell follows an inverse power-law mass dependence (k(wex) ∝ m(-γ)), where the coefficient γ is 0.05 ± 0.01 on average for all cations studied. Simulated water-exchange rates increase with temperature and decrease with increasing isotopic mass for each element. The magnitude of the water-exchange rate is different for simulations run using different water models [i.e., extended simple point charge (SPC/E) vs. four-site transferrable intermolecular potential (TIP4P)]; however, the value of the mass exponent γ is the same. Reaction rate theory calculations predict mass exponents consistent with those determined via molecular dynamics simulations. The simulation-derived mass dependences imply that solids precipitating from aqueous solution under kinetically controlled conditions should be enriched in the light isotopes of the metal cations relative to the solutions, consistent with measured isotopic signatures in natural materials and laboratory experiments. Desolvation effects are large enough that they may be a primary determinant of the observed isotopic fractionation during precipitation.
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42
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Andujar-De Sanctis IL, Singleton DA. Racing carbon atoms. Atomic motion reaction coordinates and structural effects on Newtonian kinetic isotope effects. Org Lett 2012; 14:5238-41. [PMID: 23025278 DOI: 10.1021/ol302389f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [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 methacrolein. Trajectory studies accurately predict the isotope effects and support an origin in Newton's second law of motion, with no involvement of zero-point energy or transition state recrossing. Atomic motion reaction coordinate diagrams are introduced as a way to qualitatively understand the selectivity.
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43
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Bogle XS, Singleton DA. Dynamic origin of the stereoselectivity of a nucleophilic substitution reaction. Org Lett 2012; 14:2528-31. [PMID: 22540965 DOI: 10.1021/ol300817a] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A nucleophilic substitution on a dichlorovinyl ketone was studied experimentally and computationally. A mixture of products is observed experimentally, but a conventional computational analysis does not account for the formation of the minor stereoisomer. Instead, the product mixture is predicted accurately from a dynamic trajectory study on a bifurcating energy surface. The dynamic origin of the stereoselectivity of the reaction is discussed.
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Affiliation(s)
- Xavier S Bogle
- Department of Chemistry, Texas A&M University , PO Box 30012, College Station, Texas 77842, United States
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44
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Gonzalez-James OM, Kwan EE, Singleton DA. Entropic intermediates and hidden rate-limiting steps in seemingly concerted cycloadditions. Observation, prediction, and origin of an isotope effect on recrossing. J Am Chem Soc 2012; 134:1914-7. [PMID: 22229840 DOI: 10.1021/ja208779k] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An unusual intramolecular kinetic isotope effect (KIE) in the reaction of dichloroketene with cis-2-butene does not fit with a simple asynchronous cycloaddition transition state, but it can be predicted from trajectory studies on a bifurcating energy surface. The origin of the KIE is related to a high propensity for transition state recrossing in this system, with heavier masses recrossing less. The KIE can also be predicted by a statistical model that treats the cycloaddition as a stepwise mechanism, the rate-limiting second step being associated with an entropic barrier for formation of the second carbon-carbon bond. The relevance of this stepwise mechanism to other asynchronous but seemingly concerted cycloadditions is suggested by examination of organocatalytic Diels-Alder reactions.
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Affiliation(s)
- Ollie M Gonzalez-James
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, USA
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45
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Meyer MP. New Applications of Isotope Effects in the Determination of Organic Reaction Mechanisms. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2012. [DOI: 10.1016/b978-0-12-398484-5.00002-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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46
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Itoh S, Yoshimura N, Sato M, Yamataka H. Computational Study on the Reaction Pathway of α-Bromoacetophenones with Hydroxide Ion: Possible Path Bifurcation in the Addition/Substitution Mechanism. J Org Chem 2011; 76:8294-9. [DOI: 10.1021/jo201485y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shuhei Itoh
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Nobuyoshi Yoshimura
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Makoto Sato
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Hiroshi Yamataka
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
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47
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Gonzalez-James OM, Zhang X, Datta A, Hrovat DA, Borden WT, Singleton DA. Experimental evidence for heavy-atom tunneling in the ring-opening of cyclopropylcarbinyl radical from intramolecular 12C/13C kinetic isotope effects. J Am Chem Soc 2011; 132:12548-9. [PMID: 20722415 DOI: 10.1021/ja1055593] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The intramolecular (13)C kinetic isotope effects for the ring-opening of cyclopropylcarbinyl radical were determined over a broad temperature range. The observed isotope effects are unprecedentedly large, ranging from 1.062 at 80 degrees C to 1.163 at -100 degrees C. Semiclassical calculations employing canonical variational transition-state theory drastically underpredict the observed isotope effects, but the predicted isotope effects including tunneling by a small-curvature tunneling model match well with experiment. These results and a curvature in the Arrhenius plot of the isotope effects support the recently predicted importance of heavy-atom tunneling in cyclopropylcarbinyl ring-opening.
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48
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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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49
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Abstract
Kinetic isotope effects are exquisitely sensitive probes of transition structure. As such, kinetic isotope effects offer a uniquely useful probe for the symmetry-breaking process that is inherent to stereoselective reactions. In this Concept article, we explore the role of steric and electronic effects in stereocontrol, and we relate these concepts to recent studies carried out in our laboratory. We also explore the way in which kinetic isotope effects serve as useful points of contact with computational models of transition structures. Finally, we discuss future opportunities for kinetic isotope effects to play a role in asymmetric catalyst development.
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Affiliation(s)
- Thomas Giagou
- School of Natural Sciences, University of California Merced, 5200 N. Lake Rd., Merced, CA 95344 (USA)
| | - Matthew P. Meyer
- School of Natural Sciences, University of California Merced, 5200 N. Lake Rd., Merced, CA 95344 (USA)
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50
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Ashley DC, Brinkley DW, Roth JP. Oxygen Isotope Effects as Structural and Mechanistic Probes in Inorganic Oxidation Chemistry. Inorg Chem 2010; 49:3661-75. [DOI: 10.1021/ic901778g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Daniel C. Ashley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - David W. Brinkley
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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