1
|
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.
Collapse
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
| |
Collapse
|
2
|
Abstract
The reactivity and dynamics of molecular systems can be explored computationally by classical trajectory calculations. The traditional approach involves fitting a functional form of a potential energy surface (PES) to the energies from a large number of electronic structure calculations and then integrating numerous trajectories on this fitted PES to model the molecular dynamics. The ever-decreasing cost of computing and continuing advances in computational chemistry software have made it possible to use electronic structure calculations directly in molecular dynamics simulations without first having to construct a fitted PES. In this "on-the-fly" approach, every time the energy and its derivatives are needed for the integration of the equations of motion, they are obtained directly from quantum chemical calculations. This approach started to become practical in the mid-1990s as a result of increased availability of inexpensive computer resources and improved computational chemistry software. The application of direct dynamics calculations has grown rapidly over the last 25 years and would require a lengthy review article. The present Account is limited to some of our contributions to methods development and various applications. To improve the efficiency of direct dynamics calculations, we developed a Hessian-based predictor-corrector algorithm for integrating classical trajectories. Hessian updating made this even more efficient. This approach was also used to improve algorithms for following the steepest descent reaction paths. For larger molecular systems, we developed an extended Lagrangian approach in which the electronic structure is propagated along with the molecular structure. Strong field chemistry is a rapidly growing area, and to improve the accuracy of molecular dynamics in intense laser fields, we included the time-varying electric field in a novel predictor-corrector trajectory integration algorithm. Since intense laser fields can excite and ionize molecules, we extended our studies to include electron dynamics. Specifically, we developed code for time-dependent configuration interaction electron dynamics to simulate strong field ionization by intense laser pulses. Our initial application of ab initio direct dynamics in 1994 was to CH2O → H2 + CO; the calculated vibrational distributions in the products were in very good agreement with experiment. In the intervening years, we have used direct dynamics to explore energy partitioning in various dissociation reactions, unimolecular dissociations yielding three fragments, reactions with branching after the transition state, nonstatistical dynamics of chemically activated molecules, dynamics of molecular fragmentation by intense infrared laser pulses, selective activation of specific dissociation channels by aligned intense infrared laser fields, angular dependence of strong field ionization, and simulation of sequential double ionization.
Collapse
Affiliation(s)
- H. Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Ansari AJ, Pathare RS, Maurya AK, Agnihotri VK, Khan S, Roy TK, Sawant DM, Pardasani RT. Synthesis of Diverse Nitrogen Heterocycles via
Palladium-Catalyzed Tandem Azide-Isocyanide Cross-Coupling/Cyclization: Mechanistic Insight using Experimental and Theoretical Studies. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700928] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Arshad J. Ansari
- Department of Pharmacy; Central University of Rajasthan; NH8 (Jaipur-Ajmer Highway), Bandarsindri Ajmer 305817 India
| | - Ramdas S. Pathare
- Department of Chemistry; Central University of Rajasthan; NH8 (Jaipur-Ajmer Highway), Bandarsindri Ajmer 305817 India
| | - Antim K. Maurya
- Natural Product Chemistry and Process Development division; CSIR - Institute of Himalayan Bioresource Technology, Palmpur; Himachal Pradesh 176061 India
| | - Vijai K. Agnihotri
- Natural Product Chemistry and Process Development division; CSIR - Institute of Himalayan Bioresource Technology, Palmpur; Himachal Pradesh 176061 India
| | - Shahnawaz Khan
- Department of Chemistry; Bhupal Nobles' University; Udaipur 313001 India
| | - Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences; Central University of Jammu; Jammu 180011 India
| | - Devesh M. Sawant
- Department of Pharmacy; Central University of Rajasthan; NH8 (Jaipur-Ajmer Highway), Bandarsindri Ajmer 305817 India
| | - Ram T. Pardasani
- Department of Chemistry; Central University of Rajasthan; NH8 (Jaipur-Ajmer Highway), Bandarsindri Ajmer 305817 India
| |
Collapse
|
5
|
Harabuchi Y, Ono Y, Maeda S, Taketsugu T, Keipert K, Gordon MS. Nontotally symmetric trifurcation of an
S
N
2
reaction pathway. J Comput Chem 2015; 37:487-93. [DOI: 10.1002/jcc.24241] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/06/2015] [Accepted: 10/11/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Yu Harabuchi
- Department of Chemistry, Faculty of ScienceHokkaido UniversitySapporo060‐0810 Japan
| | - Yuriko Ono
- Department of Chemistry, Faculty of ScienceHokkaido UniversitySapporo060‐0810 Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of ScienceHokkaido UniversitySapporo060‐0810 Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of ScienceHokkaido UniversitySapporo060‐0810 Japan
| | | | - Mark S. Gordon
- Department of ChemistryIowa State UniversityAmes Iowa50011
| |
Collapse
|
6
|
Harabuchi Y, Ono Y, Maeda S, Taketsugu T. Analyses of bifurcation of reaction pathways on a global reaction route map: A case study of gold cluster Au5. J Chem Phys 2015; 143:014301. [DOI: 10.1063/1.4923163] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
7
|
Ljubić I, Matasović B, Bonifačić M. An efficient buffer-mediated control between free radical substitution and proton-coupled electron transfer: dehalogenation of iodoethane by the α-hydroxyethyl radical in aqueous solution. Phys Chem Chem Phys 2013; 15:18001-11. [DOI: 10.1039/c3cp53205d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
8
|
|
9
|
A significant role of the totally symmetric valley-ridge inflection point in the bifurcating reaction pathway. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0977-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
10
|
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
| |
Collapse
|
11
|
Gas phase reactions of nitromethyl carbanion with CHCl3 and CCl4: A theoretical investigation. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
12
|
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]
|
13
|
Wang F, Sun H, Sun J, Jia X, Zhang Y, Tang Y, Pan X, Su Z, Hao L, Wang R. Mechanistic and kinetic study of CH2O+O3 reaction. J Phys Chem A 2010; 114:3516-22. [PMID: 20175584 DOI: 10.1021/jp910754b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Both singlet and triplet potential energy surfaces for the reaction of ground-state formaldehyde (CH(2)O) and ozone (O(3)) are theoretically investigated at the BMC-CCSD//BHandHLYP/6-311+G(d,p) level. Various possible isomerization and dissociation pathways are probed. Hydrogen abstraction, oxygen abstraction, and C-addition/elimination are found on both the singlet and the triplet surfaces. The major products for the total reaction are HCO and HOOO, which are generated via hydrogen abstraction. The transition state theory (TST) and multichannel RRKM calculations have been carried out for the total and individual rate constants for determinant channels over a wide range of temperatures and pressures.
Collapse
Affiliation(s)
- Fang Wang
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Renmin Road 5268, Changchun, Jilin 130024, People's Republic of China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
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]
|
15
|
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]
|
16
|
Zhou J, Schlegel B. Large nonstatistical branching ratio in the dissociation of pentane-2,4-dione radical cation: an ab initio direct classical trajectory study. J Phys Chem A 2009; 113:1453-8. [PMID: 22893922 DOI: 10.1021/jp810099b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dissociation of pentane-2,4-dione radical cation has been studied by ab initio direct classical trajectory calculations at the MP2/6-31G(d) level of theory. A bond additivity correction has been used to improve the MP2 potential energy surface (BAC-MP2). A microcanonical ensemble was constructed using quasiclassical normal-mode sampling by distributing 10 kcal/mol of excess energy above ZPE for the transition state for the tautomerization of the enol with a terminal double bond, 4-hydroxypent-4-en-2-one radical cation, to the diketo form. A total of 244 trajectories were run starting from this transition state, yielding pentane-2,4-dione radical cation and depositing energy in the terminal CC bond. As a result, the branching ratio for dissociation of the terminal CC bond versus the interior CC bonds is significantly larger than expected from RRKM theory. The branching ratio for the dissociation of the two interior CC bonds is ∼20:1, with the one closest to the activated methyl breaking more often. Since the two interior bonds are equivalent and should dissociate with equal probability, this branching ratio represents a very large deviation from statistical behavior. A simple kinetic scheme has been constructed to model the dissociation rates. The nonstatistical behavior is seen because the rate of energy flow within the molecule is comparable to or less than the rates of dissociation for the activated system. In addition to the expected dissociation products, some of the trajectories also lead to the formation of an ester-like product, prop-1-en-2-yl acetate radical cation.
Collapse
Affiliation(s)
- Jia Zhou
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | | |
Collapse
|
17
|
Zhou J, Schlegel HB. Dissociation of Acetone Radical Cation (CH3COCH3+· → CH3CO+ + CH3·): An Ab Initio Direct Classical Trajectory Study of the Energy Dependence of the Branching Ratio. J Phys Chem A 2008; 112:13121-7. [DOI: 10.1021/jp8057492] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jia Zhou
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | | |
Collapse
|
18
|
Fernandez-Ramos A, Miller JA, Klippenstein SJ, Truhlar DG. Modeling the kinetics of bimolecular reactions. Chem Rev 2007; 106:4518-84. [PMID: 17091928 DOI: 10.1021/cr050205w] [Citation(s) in RCA: 393] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Antonio Fernandez-Ramos
- Departamento de Quimica Fisica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | | | | | | |
Collapse
|