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Guo W, Kong WY, Tantillo DJ. Revisiting a classic carbocation - DFT, coupled-cluster, and ab initio molecular dynamics computations on barbaralyl cation formation and rearrangements. Chem Sci 2024; 15:d4sc04829f. [PMID: 39268206 PMCID: PMC11385376 DOI: 10.1039/d4sc04829f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
Density functional theory computations were used to model the formation and rearrangement of the barbaralyl cation (C9H+ 9). Two highly delocalized minima were located for C9H+ 9, one of C s symmetry and the other of D 3h symmetry, with the former having lower energy. Quantum chemistry-based NMR predictions affirm that the lower energy structure is the best match with experimental spectra. Partial scrambling was found to proceed through a C 2 symmetric transition structure associated with a barrier of only 2.3 kcal mol-1. The full scrambling was found to involve a C 2v symmetric transition structure associated with a 5.0 kcal mol-1 barrier. Ab initio molecular dynamics simulations initiated from the D 3h C9H+ 9 structure revealed its connection to six minima, due to the six-fold symmetry of the potential energy surface. The effects of tunneling and boron substitution on this complex reaction network were also examined.
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Affiliation(s)
- Wentao Guo
- Department of Chemistry, Univeristy of California Davis USA
| | - Wang-Yeuk Kong
- Department of Chemistry, Univeristy of California Davis USA
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2
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Feng Z, Guo W, Kong WY, Chen D, Wang S, Tantillo DJ. Analogies between photochemical reactions and ground-state post-transition-state bifurcations shed light on dynamical origins of selectivity. Nat Chem 2024; 16:615-623. [PMID: 38216753 DOI: 10.1038/s41557-023-01410-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/27/2023] [Indexed: 01/14/2024]
Abstract
Revealing the origins of kinetic selectivity is one of the premier tasks of applied theoretical organic chemistry, and for many reactions, doing so involves comparing competing transition states. For some reactions, however, a single transition state leads directly to multiple products, in which case non-statistical dynamic effects influence selectivity control. The selectivity of photochemical reactions-where crossing between excited-state and ground-state surfaces occurs near ground-state transition structures that interconvert competing products-also should be controlled by the momentum of the reacting molecules as they return to the ground state in addition to the shape of the potential energy surfaces involved. Now, using machine-learning-assisted non-adiabatic molecular dynamics and multiconfiguration pair-density functional theory, these factors are examined for a classic photochemical reaction-the deazetization of 2,3-diazabicyclo[2.2.2]oct-2-ene-for which we demonstrate that momentum dominates the selectivity for hexadiene versus [2.2.2] bicyclohexane products.
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Affiliation(s)
- Zhitao Feng
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Wentao Guo
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Wang-Yeuk Kong
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Dongjie Chen
- Department of Electrical and Computer Engineering, University of California, Davis, Davis, CA, USA
| | - Shunyang Wang
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
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3
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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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Bisht R, Popescu MV, He Z, Ibrahim AM, Crisenza GEM, Paton RS, Procter DJ. Metal-Free Arylation of Benzothiophenes at C4 by Activation as their Benzothiophene S-Oxides. Angew Chem Int Ed Engl 2023; 62:e202302418. [PMID: 37000422 PMCID: PMC10953450 DOI: 10.1002/anie.202302418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/01/2023]
Abstract
Benzothiophenes, activated by oxidation to the corresponding S-oxides, undergo C-H/C-H-type coupling with phenols to give C4 arylation products. While an electron-withdrawing group at C3 of the benzothiophene is important, the process operates without a directing group and a metal catalyst, thus rendering it compatible with sensitive functionalities-e.g. halides and formyl groups. Quantum chemical calculations suggest a formal stepwise mechanism involving heterolytic cleavage of an aryloxysulfur species to give a π-complex of the corresponding benzothiophene and a phenoxonium cation. Subsequent addition of the phenoxonium cation to the C4 position of the benzothiophene is favored over the addition to C3; Fukui functions predict that the major regioisomer is formed at the more electron-rich position between C3 and C4. Varied selective manipulation of the benzothiophene products showcase the synthetic utility of the metal-free arylation process.
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Affiliation(s)
- Ranjana Bisht
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Mihai V. Popescu
- Department of ChemistryColorado State UniversityCenter AveFort CollinsCO80523USA
| | - Zhen He
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Ameer M. Ibrahim
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | | | - Robert S. Paton
- Department of ChemistryColorado State UniversityCenter AveFort CollinsCO80523USA
| | - David J. Procter
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
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5
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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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6
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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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7
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Guo W, Hare SR, Chen SS, Saunders CM, Tantillo DJ. C-H Insertion in Dirhodium Tetracarboxylate-Catalyzed Reactions despite Dynamical Tendencies toward Fragmentation: Implications for Reaction Efficiency and Catalyst Design. J Am Chem Soc 2022; 144:17219-17231. [PMID: 36098581 DOI: 10.1021/jacs.2c07681] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rh-catalyzed C-H insertion reactions to form β-lactones suffer from post-transition state bifurcations, with the same transition states leading to ketones and ketenes via fragmentation in addition to β-lactones. In such a circumstance, traditional transition state theory cannot predict product selectivity, so we employed ab initio molecular dynamics simulations to do so and provide a framework for rationalizing the origins of said selectivity. Weak interactions between the catalyst and substrate were studied using energy decomposition and noncovalent interaction analyses, which unmasked an important role of the 2-bromophenyl substituent that has been used in multiple β-lactone-forming C-H insertion reactions. Small and large catalysts were shown to behave differently, with the latter providing a means of overcoming dynamically preferred fragmentation by lowering the barrier for the recombination of the product fragments in the grip of the large catalyst active site cavity.
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Affiliation(s)
- Wentao Guo
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Stephanie R Hare
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Shu-Sen Chen
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Carla M Saunders
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, California 95616, United States
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8
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Abstract
Differences in entropies of competing transition states can direct kinetic selectivity. Understanding and modeling such entropy differences at the molecular level is complicated by the fact that entropy is statistical in nature; i.e., it depends on multiple vibrational states of transition structures, the existence of multiple dynamically accessible pathways past these transition structures, and contributions from multiple transition structures differing in conformation/configuration. The difficulties associated with modeling each of these contributors are discussed here, along with possible solutions, all with an eye toward the development of portable qualitative models of use to experimentalists aiming to design reactions that make use of entropy to control kinetic selectivity.
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Affiliation(s)
- Dean J Tantillo
- Department of Chemistry, University of California-Davis, 1 Shields Ave, Davis, California 95616, United States
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9
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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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10
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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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11
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Tantillo DJ. Dynamic effects on organic reactivity—Pathways to (and from) discomfort. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Dean J. Tantillo
- Department of Chemistry University of California, Davis Davis California USA
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12
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Feng Z, Tantillo DJ. Dynamic Effects on Migratory Aptitudes in Carbocation Reactions. J Am Chem Soc 2021; 143:1088-1097. [PMID: 33400509 DOI: 10.1021/jacs.0c11850] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Carbocation rearrangement reactions are of great significance to synthetic and biosynthetic chemistry. In pursuit of a scale of inherent migratory aptitude that takes into account dynamic effects, both uphill and downhill ab initio molecular dynamics (AIMD) simulations were used to examine competing migration events in a model system designed to remove steric and electronic biases. The results of these simulations were combined with detailed investigations of potential energy surface topography and variational transition state theory calculations to reveal the importance of nonstatistical dynamic effects on migratory aptitude.
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Affiliation(s)
- Zhitao Feng
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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