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Carpenter BK. An argument for abandoning the "allowed" and "forbidden" classification of electrocyclic reactions. Chem Sci 2025:d4sc08748h. [PMID: 39981038 PMCID: PMC11837749 DOI: 10.1039/d4sc08748h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2024] [Accepted: 01/23/2025] [Indexed: 02/22/2025] Open
Abstract
The division of electrocyclic reactions into "allowed" and "forbidden" classes carries the implication that reactions of the latter class are so energetically penalised that they will occur only if their "allowed" alternatives are rendered effectively impossible. The present work tests that assumption, using NEVPT2 and DFT calculations on a variety of cyclobutene ring openings and (Z)-1,3,5-hexatriene ring closures, and their benzannelated congeners. The results show the assumption to be incorrect. The potential energy differences between "forbidden" and "allowed" transition states are found to cover a wide range of values, with the smallest being less than half the classical barrier to internal rotation of ethane. It follows that planning a total synthesis on the presumption that electrocyclic reactions will always follow the "allowed" stereochemical course is an unreliable strategy because other commonly occurring factors, such as routine steric and electronic substituent effects, can easily outweigh the electronic penalty for following the nominally forbidden mechansim. A particular case involving a proposed synthetic route to a class of anticancer compounds is highlighted as an example.
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Lee J, Tantillo DJ, Wang LP, Fiehn O. Predicting Collision-Induced-Dissociation Tandem Mass Spectra (CID-MS/MS) Using Ab Initio Molecular Dynamics. J Chem Inf Model 2024; 64:7470-7487. [PMID: 39329407 PMCID: PMC11492810 DOI: 10.1021/acs.jcim.4c00760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
Compound identification is at the center of metabolomics, usually by comparing experimental mass spectra against library spectra. However, most compounds are not commercially available to generate library spectra. Hence, for such compounds, MS/MS spectra need to be predicted. Machine learning and heuristic models have largely failed except for lipids. Here, quantum chemistry software can be used to predict mass spectra. However, quantum chemistry predictions for collision induced dissociation (CID) mass spectra in LC-MS/MS are rare. We present the CIDMD (Collision-Induced Dissociation via Molecular Dynamics) framework to model CID-based MS/MS spectra. It uses first-principles molecular dynamics (MD) to simulate the physical process of molecular collisions in CID tandem mass spectrometry. First, molecular ions are constructed at specific protonation sites. Using density functional theory, these protonated ions are targeted by argon collider gas atoms at user-specified velocities. Subsequent bond breakages are simulated over time for at least 1,000 fs. Each simulation is repeated multiple times from various collisional directions. Fragmentations are accumulated over those repeated collisions to generate CIDMD in silico mass spectra. Twelve small metabolites (<205 Da) were selected to test the accuracy of this framework in comparison to experimental MS/MS spectra. When testing different protomers, collider velocities, number of simulations, simulation time and impact factor b cutoffs, we yielded 261 predicted mass spectra. These in silico spectra resulted in entropy similarity scores of an average 624 ± 189 for all 261 spectra compared to their corresponding experimental spectra, which improved to 828 ± 77 when using optimal parameters of the most probable protomers for 12 molecules. With increasing molecular mass, higher velocities achieved better results. Similarly, different protomers showed large differences in fragmentation; hence, with increasing numbers of protomers and tautomers, the average CIDMD prediction accuracy decreased. Mechanistic details showed that specific fragment ions can be produced from different protomers via multiple fragmentation pathways. We propose that CIDMD is a suitable tool to predict mass spectra of small metabolites like produced by the gut microbiome.
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Affiliation(s)
- Jesi Lee
- Department of Chemistry, University of California, Davis, California 95616, United States
- West Coast Metabolomics Center, University of California, Davis, California 95616, United States
| | - Dean Joseph Tantillo
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, California 95616, 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: 7] [Impact Index Per Article: 3.5] [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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Lee S, Goodman JM. VRAI-selectivity: calculation of selectivity beyond transition state theory. Org Biomol Chem 2021; 19:3940-3947. [PMID: 33949564 DOI: 10.1039/d1ob00234a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In recent years, a growing number of organic reactions in the literature have shown selectivity controlled by reaction dynamics rather than by transition state theory. Such reactions are difficult to analyse because the transition state theory approach often does not capture the subtlety of the energy landscapes the compounds traverse and, therefore, cannot accurately predict the selectivity. We present an algorithm that can predict the major product and selectivity for a wide range of potential energy surfaces where the product distribution is influenced by reaction dynamics. The method requires as input calculation of the transition states, the intermediate (if present) and the product geometries. The algorithm is quick and simple to run and, except for two reactions with long alkyl chains, calculates selectivity more accurately than transition state theory alone.
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Affiliation(s)
- Sanha Lee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Jonathan M Goodman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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Laconsay CJ, Mallick D, Shaik S. External Electric Fields Interrupt the Concerted Cope Rearrangement of Semibullvalene. J Org Chem 2020; 86:731-738. [PMID: 33280381 DOI: 10.1021/acs.joc.0c02322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The topic of this paper is whether the mechanism of the degenerate Cope rearrangement of semibullvalene can be affected by the presence of electrostatic fields. Herein, we report that the shape of the energy surface, as demonstrated by an "interrupted" (stepwise) mechanism, is altered in the presence of a copper cation, Cu+. Natural bond-orbital and block-localized wave-function energy decomposition analyses suggest that orbital and electrostatic interactions play a major role in altering the shape of the energy surface. Applying additional external electric fields (EEFs) induces a significant change to the energy surface with Cu+ present but negligible effects in the absence of Cu+. These findings are consistent with recent studies that demonstrate that EEFs more readily stabilize/destabilize systems with larger, more polarizable, dipole moments.
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Affiliation(s)
- Croix J Laconsay
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel.,Department of Chemistry, University of California-Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Dibyendu Mallick
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel.,Department of Chemistry, Presidency University, Kolkata 700073, India
| | - Sason Shaik
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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Zheng C. Divergent Pathways and Dynamic Effects of Intramolecular Hydride Transfer Reactions Mediated by Cp*M(
III
) Complexes (M = Co, Rh, Ir)
†. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Chao Zheng
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Lu Shanghai 200032 China
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Zheng C, You SL. Exploring the Chemistry of Spiroindolenines by Mechanistically-Driven Reaction Development: Asymmetric Pictet-Spengler-type Reactions and Beyond. Acc Chem Res 2020; 53:974-987. [PMID: 32275392 DOI: 10.1021/acs.accounts.0c00074] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Pictet-Spengler reaction is a fundamental named reaction in organic chemistry, and it is the most straightforward method for the synthesis of tetrahydro-β-carbolines, a core structure embedded in numerous alkaloids. Spiroindolenines are often proposed as possible intermediates in Pictet-Spengler reactions. However, whether the spiroindolenine species is an intermediate in the mechanism of the asymmetric Pictet-Spengler reaction remains unclear. Questions about the role of the spiroindolenine species regarding the mechanism include the following: Can the spiroindolenine species be formed effectively under Pictet-Spengler conditions? If so, what is its fate? Is the delivery of the enantioenriched tetrahydro-β-carboline product related to the spiroindolenine intermediate? Previous studies regarding these questions have not reached a consensus. Therefore, elucidating these questions will advance the field of synthetic organic chemistry.The first highly enantioselective synthesis of spiroindolenines that have the same molecular scaffold as the proposed key intermediate of the Pictet-Spengler reaction was accomplished by an Ir-catalyzed intramolecular asymmetric allylic substitution reaction of an indol-3-yl allylic carbonate. In this reaction, a piperidine, pyrrolidine, or cyclopentane ring can be introduced in conjunction with the indolenine structure.Spiroindolenines were found to undergo ring-expansive migration reactions when treated with a catalytic amount of an acid, leading to tetrahydro-β-carbolines or related tetrahydrocarbazoles. Comprehensive DFT calculations and Born-Oppenheimer molecular dynamics simulations have provided insight into the mechanism of the migration process. It has been found that the stereochemistry is strongly correlated with the electronic properties of the migratory group along with the acidity of the catalyst. Close interactions between the positively charged migratory group and the electron-rich indole ring favor the stereospecificity of the migration. Furthermore, a continuous mechanistic spectrum of the Pictet-Spengler reactions can be obtained on the basis of two readily accessible energetic parameters that are derived from computed energies for competing transition states relative to a key intermediate species. This theoretical model provides a unified mechanistic understanding of the asymmetric Pictet-Spengler reaction, which has been further supported by rationally designed prototype reactions. Chemically and stereochemically controllable migration can be achieved when multiple potential migratory groups are available.The reactivity of spiroindolenines has also been explored beyond Pictet-Spengler reactions. A one-pot Ir-catalyzed asymmetric allylic dearomatization/stereoconvergent migration allows the facile synthesis of enantioenriched tetrahydro-β-carbolines from racemic starting materials. An unprecedented six- to seven-membered ring-expansive migration can be achieved when a vinyliminium moiety is involved as a highly reactive migratory group. This reaction facilitates the stereoselective synthesis of thermodynamically challenging indole-annulated seven-membered rings. It has also been found that the migration process can be interrupted. The electrophilic migratory group released from the retro-Mannich reaction of a spiroindolenine can be captured by an inter- or intramolecular nucleophile, thus providing new entries into structurally diverse polycyclic indole derivatives.Therefore, the mechanism of the Pictet-Spengler reaction can be probed by manipulating the reactivity of the spiroindolenine species. In turn, the mechanistic insights gained herein will aid in chemical transformations toward various target molecules. This study serves as a vivid example of the positive interplay between experimental and theoretical investigations in synthetic organic chemistry.
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Affiliation(s)
- Chao Zheng
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Shu-Li You
- State Key Laboratory of Organometallic Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
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Stereoselective synthesis of medium lactams enabled by metal-free hydroalkoxylation/stereospecific [1,3]-rearrangement. Nat Commun 2019; 10:3234. [PMID: 31324800 PMCID: PMC6642132 DOI: 10.1038/s41467-019-11245-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 07/02/2019] [Indexed: 12/23/2022] Open
Abstract
Rearrangement reactions have attracted considerable interest over the past decades due to their high bond-forming efficiency and atom economy in the construction of complex organic architectures. In contrast to the well-established [3,3]-rearrangement, [1,3] O-to-C rearrangement has been far less vigorously investigated, and stereospecific [1,3]-rearrangement is extremely rare. Here, we report a metal-free intramolecular hydroalkoxylation/[1,3]-rearrangement, leading to the practical and atom-economical assembly of various valuable medium-sized lactams with wide substrate scope and excellent diastereoselectivity. Moreover, such an asymmetric cascade cyclization has also been realized by chiral Brønsted acid-catalyzed kinetic resolution. In addition, biological tests reveal that some of these medium-sized lactams displayed their bioactivity as antitumor agents against melanoma cells, esophageal cancer cells and breast cancer cells. A mechanistic rationale for the reaction is further supported by control experiments and theoretical calculations. Stereospecific [1,3]-rearrangements are rarely reported method to efficiently build complex organic architectures. Here, the authors describe a metal-free intramolecular hydroalkoxylation/[1,3]-rearrangement sequence affording medium-sized lactams with wide scope, also in an asymmetric fashion.
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Yang Z, Jamieson CS, Xue XS, Garcia-Borràs M, Benton T, Dong X, Liu F, Houk K. Mechanisms and Dynamics of Reactions Involving Entropic Intermediates. TRENDS IN CHEMISTRY 2019. [DOI: 10.1016/j.trechm.2019.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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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: 0.1] [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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11
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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: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Mandal N, Datta A. Gold(I)-Catalyzed Intramolecular Diels–Alder Reaction: Evolution of Trappable Intermediates via Asynchronous Transition States. J Org Chem 2018; 83:11167-11177. [DOI: 10.1021/acs.joc.8b01752] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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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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: 42] [Impact Index Per Article: 6.0] [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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