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Karmakar S, Keshavamurthy S. Intramolecular vibrational energy redistribution and the quantum ergodicity transition: a phase space perspective. Phys Chem Chem Phys 2020; 22:11139-11173. [DOI: 10.1039/d0cp01413c] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The onset of facile intramolecular vibrational energy flow can be related to features in the connected network of anharmonic resonances in the classical phase space.
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Affiliation(s)
- Sourav Karmakar
- Department of Chemistry
- Indian Institute of Technology
- Kanpur
- India
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2
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Yan B, Fu Y, Zhu H, Chen Z. Synthesis of Divergent Benzo[b]fluorenones through Cycloaromatization Reactions of 1,5-Enynols and 1,5-Diynols. J Org Chem 2019; 84:4246-4262. [DOI: 10.1021/acs.joc.9b00231] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | | | | | - Zhiyuan Chen
- Key Laboratory of Functional Small Organic Molecules, Ministry of Education, and College of Chemistry & Chemical Engineering, Jiangxi Normal University, Nanchang, Jiangxi 330022, China
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3
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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: 2.5] [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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Rana A, Paul I, Schmittel M. Dynamic effects in the didehydro-Diels-Alder (DDDA) reaction of enyne-ketoenes: 50% stepwise bond formation in spite of concerted transition state. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Anup Rana
- Department of Chemistry and Biology; Universität Siegen; Siegen Germany
| | - Indrajit Paul
- Department of Chemistry and Biology; Universität Siegen; Siegen Germany
| | - Michael Schmittel
- Department of Chemistry and Biology; Universität Siegen; Siegen Germany
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Li Y, Kirillov AM, Fang R, Yang L. Effect of Substituent on the Mechanism and Chemoselectivity of the Gold(I)-Catalyzed Propargyl Ester Tandem Cyclization. Organometallics 2017. [DOI: 10.1021/acs.organomet.7b00042] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yunhe Li
- State
Key Laboratory of Applied Organic Chemistry and Key Laboratory of
Nonferrous Metals Chemistry and Resources Utilization of Gansu Province,
College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Alexander M. Kirillov
- Centro
de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Ran Fang
- State
Key Laboratory of Applied Organic Chemistry and Key Laboratory of
Nonferrous Metals Chemistry and Resources Utilization of Gansu Province,
College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Lizi Yang
- State
Key Laboratory of Applied Organic Chemistry and Key Laboratory of
Nonferrous Metals Chemistry and Resources Utilization of Gansu Province,
College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
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Carpenter BK, Harvey JN, Orr-Ewing AJ. The Study of Reactive Intermediates in Condensed Phases. J Am Chem Soc 2016; 138:4695-705. [DOI: 10.1021/jacs.6b01761] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Barry K. Carpenter
- School
of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
| | - Jeremy N. Harvey
- Department
of Chemistry, KU Leuven, Celestijnen Laan 200F, B-3001 Heverlee, Belgium
| | - Andrew J. Orr-Ewing
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
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Rana A, Cinar ME, Samanta D, Schmittel M. Solving the puzzling competition of the thermal C(2)-C(6) vs Myers-Saito cyclization of enyne-carbodiimides. Beilstein J Org Chem 2016; 12:43-9. [PMID: 26877807 PMCID: PMC4734315 DOI: 10.3762/bjoc.12.6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/24/2015] [Indexed: 11/23/2022] Open
Abstract
The mechanism of the thermal cyclization of enyne-carbodiimides 7a–c has been studied computationally by applying the DFT method. The results indicate that enyne-carbodiimides preferentially follow the C2–C6 (Schmittel) cyclization pathway in a concerted fashion although the Myers–Saito diradical formation is kinetically preferred. The experimentally verified preference of the C2–C6 over the Myers–Saito pathway is guided by the inability of the Myers–Saito diradical to kinetically compete in the rate-determining trapping reactions, either inter- or intramolecular, with the concerted C2–C6 cyclization. As demonstrated with enyne-carbodiimide 11, the Myers–Saito channel can be made the preferred pathway if the trapping reaction by hydrogen transfer is no more rate determining.
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Affiliation(s)
- Anup Rana
- Department of Chemistry and Biology, Universität Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Mehmet Emin Cinar
- Department of Chemistry and Biology, Universität Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Debabrata Samanta
- Department of Chemistry and Biology, Universität Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Michael Schmittel
- Department of Chemistry and Biology, Universität Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
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Petraglia R, Nicolaï A, Wodrich MD, Ceriotti M, Corminboeuf C. Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry. J Comput Chem 2016; 37:83-92. [PMID: 26228927 PMCID: PMC5324590 DOI: 10.1002/jcc.24025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 06/30/2015] [Accepted: 06/30/2015] [Indexed: 01/09/2023]
Abstract
Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a multitude of molecular conformations exists on incredibly complex potential energy surfaces (PES). Here, we borrow a computational technique originally conceived to be used in the context of biological simulations, together with empirical force fields, and apply it to organic chemical problems. Replica-exchange molecular dynamics (REMD) permits thorough exploration of the PES. We combined REMD with density functional tight binding (DFTB), thereby establishing the level of accuracy necessary to analyze small molecular systems. Through the study of four prototypical problems: isomer identification, reaction mechanisms, temperature-dependent rotational processes, and catalysis, we reveal new insights and chemistry that likely would be missed using static electronic structure computations. The REMD-DFTB methodology at the heart of this study is powered by i-PI, which efficiently handles the interface between the DFTB and REMD codes.
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Affiliation(s)
- Riccardo Petraglia
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Adrien Nicolaï
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Matthew D Wodrich
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Michele Ceriotti
- Laboratory of Computational Science and Modelling, Institut des Materiaux, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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Abstract
The thermal cyclization of enyne-carbodiimides substituted at both the alkyne and carbodiimide terminus showed two curved Hammett correlations (log k/k0 against σp) that were fully reproduced by DFT (density functional theory) computational results. The latter suggest a concerted mechanism, but the transition state (TS) analysis failed to reveal any mechanistic insight about the reason for a curved Hammett correlation. Instead a preTS inspection, i.e., examination of the electronic and steric details on route between reactant and TS, furnished a detailed picture of the mechanism.
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Affiliation(s)
- Anup Rana
- Department of Chemistry and Biology, Organische Chemie 1, Universität Siegen , Adolf-Reichwein-Strasse 2, D-57068 Siegen, Germany
| | - M Emin Cinar
- Department of Chemistry and Biology, Organische Chemie 1, Universität Siegen , Adolf-Reichwein-Strasse 2, D-57068 Siegen, Germany
| | - Debabrata Samanta
- Department of Chemistry and Biology, Organische Chemie 1, Universität Siegen , Adolf-Reichwein-Strasse 2, D-57068 Siegen, Germany
| | - Michael Schmittel
- Department of Chemistry and Biology, Organische Chemie 1, Universität Siegen , Adolf-Reichwein-Strasse 2, D-57068 Siegen, Germany
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