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Yang Z, Doubleday C, Houk KN. QM/MM Protocol for Direct Molecular Dynamics of Chemical Reactions in Solution: The Water-Accelerated Diels–Alder Reaction. J Chem Theory Comput 2015; 11:5606-12. [DOI: 10.1021/acs.jctc.5b01029] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhongyue Yang
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Charles Doubleday
- Department
of Chemistry, Columbia University, 3000 Broadway,
MC 3142, New York, New York 10027, United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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2
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Tagawa K, Sasagawa K, Wakisaka K, Monjiyama S, Katayama M, Yamataka H. Experimental Study on the Reaction Pathway of α-Haloacetophenones with NaOMe: Examination of Bifurcation Mechanism. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20130253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Kohei Tagawa
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University
| | - Keita Sasagawa
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University
| | - Ken Wakisaka
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University
| | - Shunsuke Monjiyama
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University
| | - Mika Katayama
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University
| | - Hiroshi Yamataka
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University
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3
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Mizutani T, Jinguji M, Yamataka H. Reaction Pathways and Dynamics Effects for Ionizations of Vinyl Diazonium Ions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2012. [DOI: 10.1246/bcsj.20120124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomoyuki Mizutani
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University
| | - Masaru Jinguji
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University
| | - Hiroshi Yamataka
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University
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4
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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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5
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Yamamoto Y, Hasegawa H, Yamataka H. Dynamic Path Bifurcation in the Beckmann Reaction: Support from Kinetic Analyses. J Org Chem 2011; 76:4652-60. [DOI: 10.1021/jo200728t] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yutaro Yamamoto
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro, Toshima-ku 171-8501 Tokyo, Japan
| | - Hiroto Hasegawa
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro, Toshima-ku 171-8501 Tokyo, Japan
| | - Hiroshi Yamataka
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro, Toshima-ku 171-8501 Tokyo, Japan
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6
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Itoh S, Yamataka H. Dynamics Effects on an E2/E1cb Borderline Mechanism: Unimolecular Elimination of 2-Aryl-3-chloro-2-R-propanols. Chemistry 2010; 17:1230-7. [DOI: 10.1002/chem.201001926] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Indexed: 11/08/2022]
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7
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Katori T, Itoh S, Sato M, Yamataka H. Reaction Pathways and Possible Path Bifurcation for the Schmidt Reaction. J Am Chem Soc 2010; 132:3413-22. [DOI: 10.1021/ja908899u] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tetsuji Katori
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro, Toshima-ku 171-8501 Tokyo, Japan
| | - Shuhei Itoh
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro, Toshima-ku 171-8501 Tokyo, Japan
| | - Makoto Sato
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro, Toshima-ku 171-8501 Tokyo, Japan
| | - Hiroshi Yamataka
- Department of Chemistry and the Research Center for Smart Molecules, Rikkyo University, Nishi-Ikebukuro, Toshima-ku 171-8501 Tokyo, Japan
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8
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Molecular dynamics simulations and mechanism of organic reactions: non-TST behaviors. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0065-3160(08)44004-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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9
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Yamataka H, Sato M, Hasegawa H, Ammal SC. Dynamic path bifurcation for the Beckmann reaction: observation and implication. Faraday Discuss 2010. [DOI: 10.1039/b906159b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Houmam A. Electron Transfer Initiated Reactions: Bond Formation and Bond Dissociation. Chem Rev 2008; 108:2180-237. [PMID: 18620366 DOI: 10.1021/cr068070x] [Citation(s) in RCA: 199] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Arnaut LG, Formosinho SJ. The rates of S(N)2 reactions and their relation to molecular and solvent properties. Chemistry 2007; 13:8018-28. [PMID: 17616960 DOI: 10.1002/chem.200700276] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The energy barriers of symmetrical methyl exchanges in the gas phase have been calculated with the reaction path of the intersecting/interacting-state model (ISM). Reactive bond lengths increase down a column of the Periodic Table and compensate for the decrease in the force constants, which explains the near constancy of the intrinsic barriers in the following series of nucleophiles: F(-) approximately Cl(-) approximately Br(-) approximately I(-). This compensation is absent along the rows of the Periodic Table and the trend in the reactivity is dominated by the increase in the electrophilicity index of the nucleophile in the series C<N<O<F. Solvent effects have been quantitatively incorporated into the ISM model through a correlation between electrophilicity and the solvent acceptor number. This correlation is transferable between nucleophiles and solvents and allows the methyl transfer rate constants in solution to be calculated with remarkable simplicity and accuracy. The relationship between the S(N)2 and electron-transfer mechanisms is clarified and it is shown that smaller solvent static effects should be expected for electron transfer in the absence of a thermodynamic driving force.
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Affiliation(s)
- Luis G Arnaut
- Chemistry Department, University of Coimbra, P-3049 Coimbra Codex, Portugal.
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12
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Schmittel M, Vavilala C, Jaquet R. Elucidation of nonstatistical dynamic effects in the cyclization of enyne allenes by means of kinetic isotope effects. Angew Chem Int Ed Engl 2007; 46:6911-4. [PMID: 17680572 DOI: 10.1002/anie.200700709] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Michael Schmittel
- FB 8 (Chemie - Biologie), Universität Siegen, Adolf-Reichwein-Strasse 2, 57068 Siegen, Germany.
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13
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Schmittel M, Vavilala C, Jaquet R. Charakterisierung nichtstatistischer dynamischer Effekte in der Cyclisierung von Eninallenen mittels kinetischer Isotopeneffekte. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700709] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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14
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Tachikawa H. Direct ab initio molecular dynamics study on a microsolvated SN2 reaction of OH-(H2O) with CH3Cl. J Chem Phys 2007; 125:133119. [PMID: 17029445 DOI: 10.1063/1.2229208] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Reaction dynamics for a microsolvated SN2 reaction OH-(H2O)+CH3Cl have been investigated by means of the direct ab initio molecular dynamics method. The relative center-of-mass collision energies were chosen as 10, 15, and 25 kcal/mol. Three reaction channels were found as products. These are (1) a channel leading to complete dissociation (the products are CH3OH+Cl- +H2O: denoted by channel I), (2) a solvation channel (the products are Cl-(H2O)+CH3OH: channel II), and (3) a complex formation channel (the products are CH3OH...H2O+Cl-: channel III). The branching ratios for the three channels were drastically changed as a function of center-of-mass collision energy. The ratio of complete dissociation channel (channel I) increased with increasing collision energy, whereas that of channel III decreased. The solvation channel (channel II) was minor at all collision energies. The selectivity of the reaction channels and the mechanism are discussed on the basis of the theoretical results.
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Affiliation(s)
- Hiroto Tachikawa
- Division of Materials Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan.
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15
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Li J, Shaik S, Schlegel HB. A Single Transition State Serves Two Mechanisms. The Branching Ratio for CH2O•- + CH3Cl on Improved Potential Energy Surfaces. J Phys Chem A 2006; 110:2801-6. [PMID: 16494392 DOI: 10.1021/jp0563336] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction of formaldehyde radical anion with methyl chloride, CH2O*- + CH3Cl, is an example in which a single transition state leads to two products: substitution at carbon (Sub(C), CH3CH2O* + Cl-) and electron transfer (ET, CH2O + CH3* + Cl-). The branching ratio for this reaction has been studied by ab initio molecular dynamics (AIMD). The energies of transition states and intermediates were computed at a variety of levels of theory and compared to accurate energetics calculated by the G3 and CBS-QB3 methods. A bond additivity correction has been constructed to improve the Hartree-Fock potential energy surface (BAC-UHF). A satisfactory balance between good energetics and affordable AIMD calculations can be achieved with BH&HLYP/6-31G(d) and BAC-UHF/6-31G(d) calculations. Approximately 200 ab initio classical trajectories were calculated for each level of theory with initial conditions sampled from a thermal distribution at 298 K at the transition state. Three types of trajectories were distinguished: trajectories that go directly to ET product, trajectories that go to Sub(C) product, and trajectories that initially go into the Sub(C) valley and then dissociate to ET products. The BH&HLYP/6-31G(d) calculations overestimate the number of nonreactive and direct ET trajectories because the transition state is too early. For the BH&HLYP and BAC-UHF methods, about one-third of the trajectories that initially go into the Sub(C) valley dissociate to ET products, compared to just over half with UHF/6-31G(d) in the earlier study. This difference can be attributed to a better value for the calculated energy release from the initial transition state and to an improved Sub(C) --> ET barrier height with the BH&HLYP and BAC-UHF methods.
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Affiliation(s)
- Jie Li
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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16
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Doubleday C, Suhrada CP, Houk KN. Dynamics of the Degenerate Rearrangement of Bicyclo[3.1.0]hex-2-ene. J Am Chem Soc 2005; 128:90-4. [PMID: 16390135 DOI: 10.1021/ja050722w] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quasiclassical direct dynamics simulations are applied to a 4-fold degenerate rearrangement which yields a nonstatistical product distribution. The simulated product ratio agrees with experiment and is found to be entirely dynamically determined. Trajectory lifetimes are on the order of a low-frequency vibrational period. The interaction of reaction momentum with the geometric features of the potential surface produces selectivity despite a common energy barrier. A geometric model is described for qualitatively estimating much of the dynamically determined product ratio independently of trajectory calculations. The characteristics of this reaction are expected also to apply to others involving modestly stabilized diradical intermediates.
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Affiliation(s)
- Charles Doubleday
- Department of Chemistry, Columbia University, New York, NY 10027, USA.
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Abstract
A brief review is presented of post-RRKM models for unimolecular reaction kinetics. The dynamics of the gas-phase S(N)2 reaction are discussed, and the important role of phase-space bottlenecks is highlighted. The remainder of the review is devoted to experimental and trajectory simulation results on thermal reactions of organic molecules that exhibit nonstatistical dynamics quite unlike that seen in the S(N)2 reaction. Specifically, the intermediates generated in these reactions decay much faster than RRKM theory would predict, and often with bimodal or multimodal lifetime distributions. A qualitative model for this behavior based on overlaps of transitional regions in the molecular phase space is discussed.
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Affiliation(s)
- Barry K Carpenter
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853-1301, USA.
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18
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Li J, Li X, Shaik S, Schlegel HB. Single Transition State Serves Two Mechanisms. Ab Initio Classical Trajectory Calculations of the Substitution−Electron Transfer Branching Ratio in CH2O•- + CH3Cl. J Phys Chem A 2004. [DOI: 10.1021/jp046827n] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jie Li
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, Department of Organic Chemistry, Hebrew University, Jerusalem 91904, Israel, and the Lise Meitner-Minerva Center of Computational Chemistry, Hebrew University, Jerusalem 91904, Israel
| | - Xiaosong Li
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, Department of Organic Chemistry, Hebrew University, Jerusalem 91904, Israel, and the Lise Meitner-Minerva Center of Computational Chemistry, Hebrew University, Jerusalem 91904, Israel
| | - Sason Shaik
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, Department of Organic Chemistry, Hebrew University, Jerusalem 91904, Israel, and the Lise Meitner-Minerva Center of Computational Chemistry, Hebrew University, Jerusalem 91904, Israel
| | - H. Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, Department of Organic Chemistry, Hebrew University, Jerusalem 91904, Israel, and the Lise Meitner-Minerva Center of Computational Chemistry, Hebrew University, Jerusalem 91904, Israel
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