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Gantzer P, Staub R, Harabuchi Y, Maeda S, Varnek A. Chemography-guided analysis of a reaction path network for ethylene hydrogenation with a model Wilkinson's catalyst. Mol Inform 2024:e202400063. [PMID: 39121023 DOI: 10.1002/minf.202400063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 07/11/2024] [Accepted: 07/19/2024] [Indexed: 08/11/2024]
Abstract
Visualization and analysis of large chemical reaction networks become rather challenging when conventional graph-based approaches are used. As an alternative, we propose to use the chemical cartography ("chemography") approach, describing the data distribution on a 2-dimensional map. Here, the Generative Topographic Mapping (GTM) algorithm - an advanced chemography approach - has been applied to visualize the reaction path network of a simplified Wilkinson's catalyst-catalyzed hydrogenation containing some 105 structures generated with the help of the Artificial Force Induced Reaction (AFIR) method using either Density Functional Theory or Neural Network Potential (NNP) for potential energy surface calculations. Using new atoms permutation invariant 3D descriptors for structure encoding, we've demonstrated that GTM possesses the abilities to cluster structures that share the same 2D representation, to visualize potential energy surface, to provide an insight on the reaction path exploration as a function of time and to compare reaction path networks obtained with different methods of energy assessment.
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Affiliation(s)
- Philippe Gantzer
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido, 001-0021, Japan
| | - Ruben Staub
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido, 001-0021, Japan
| | - Yu Harabuchi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido, 001-0021, Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido, 001-0021, Japan
| | - Alexandre Varnek
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido, 001-0021, Japan
- Laboratory of Chemoinformatics, UMR 7140, CNRS, University of Strasbourg, Strasbourg, 67081, France
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Tasi DA, Czakó G. Benchmark ab initio characterization of the complex potential energy surfaces of the HOO - + CH 3Y [Y = F, Cl, Br, I] reactions. Phys Chem Chem Phys 2024; 26:16048-16059. [PMID: 38779842 DOI: 10.1039/d4cp01071j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
The α-effect is a well-known phenomenon in organic chemistry, and is related to the enhanced reactivity of nucleophiles involving one or more lone-pair electrons adjacent to the nucleophilic center. The gas-phase bimolecular nucleophilic substitution (SN2) reactions of α-nucleophile HOO- with methyl halides have been thoroughly investigated experimentally and theoretically; however, these investigations have mainly focused on identifying and characterizing the α-effect of HOO-. Here, we perform the first comprehensive high-level ab initio mapping for the HOO- + CH3Y [Y = F, Cl, Br and I] reactions utilizing the modern explicitly-correlated CCSD(T)-F12b method with the aug-cc-pVnZ [n = 2-4] basis sets. The present ab initio characterization considers five distinct product channels of SN2: (CH3OOH + Y-), proton abstraction (CH2Y- + H2O2), peroxide ion substitution (CH3OO- + HY), SN2-induced elimination (CH2O + HY + HO-) and SN2-induced rearrangement (CH2(OH)O- + HY). Moreover, besides the traditional back-side attack Walden inversion, the pathways of front-side attack, double inversion and halogen-bond complex formation have also been explored for SN2. With regard to the Walden inversion of HOO- + CH3Cl, the previously unaddressed discrepancies concerning the geometry of the corresponding transition state are clarified. For the HOO- + CH3F reaction, the recently identified SN2-induced elimination is found to be more exothermic than the SN2 channel, submerged by ∼36 kcal mol-1. The accuracy of our high-level ab initio calculations performed in the present study is validated by the fact that our new benchmark 0 K reaction enthalpies show excellent agreement with the experimental data in nearly all cases.
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Affiliation(s)
- Domonkos A Tasi
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Gábor Czakó
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
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Teramoto H, Saito T, Aoki M, Murayama B, Kobayashi M, Nakamura T, Taketsugu T. Reproducing the Reaction Route Map on the Shape Space from Its Quotient by the Complete Nuclear Permutation-Inversion Group. J Chem Theory Comput 2023; 19:5886-5896. [PMID: 37642714 DOI: 10.1021/acs.jctc.3c00500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
This study develops an algorithm to reproduce reaction route maps (RRMs) in the shape space from the outputs of potential search algorithms. To demonstrate the algorithm, global reaction route mapping is utilized as a potential search algorithm, but the proposed algorithm should work with other potential search algorithms in principle. The proposed algorithm does not require any encoding of the molecular configurations and is thus applicable to complicated realistic molecules for which efficient encoding is not readily available. We show that subgraphs of an RRM mapped to each other by the action of the symmetry group are isomorphic and also provide an algorithm to compute the set of feasible transformations in the sense of Longuet-Higgins. We demonstrate the proposed algorithm in toy models and in more realistic molecules. Finally, we remark on absolute rate theory from our perspective.
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Affiliation(s)
- Hiroshi Teramoto
- Faculty of Engineering Science, Kansai University, Suita 564-8680, Japan
| | - Takuya Saito
- Department of Mathematics, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Department of Economics and Statistics, University of Turin, 10124 Turin, Italy
| | - Masamitsu Aoki
- Department of Mathematics, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Burai Murayama
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Masato Kobayashi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- WPI-ICReDD, Hokkaido University, Sapporo 001-0021, Japan
| | - Takenobu Nakamura
- National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8568, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- WPI-ICReDD, Hokkaido University, Sapporo 001-0021, Japan
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Staub R, Gantzer P, Harabuchi Y, Maeda S, Varnek A. Challenges for Kinetics Predictions via Neural Network Potentials: A Wilkinson's Catalyst Case. Molecules 2023; 28:molecules28114477. [PMID: 37298952 DOI: 10.3390/molecules28114477] [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: 04/02/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Ab initio kinetic studies are important to understand and design novel chemical reactions. While the Artificial Force Induced Reaction (AFIR) method provides a convenient and efficient framework for kinetic studies, accurate explorations of reaction path networks incur high computational costs. In this article, we are investigating the applicability of Neural Network Potentials (NNP) to accelerate such studies. For this purpose, we are reporting a novel theoretical study of ethylene hydrogenation with a transition metal complex inspired by Wilkinson's catalyst, using the AFIR method. The resulting reaction path network was analyzed by the Generative Topographic Mapping method. The network's geometries were then used to train a state-of-the-art NNP model, to replace expensive ab initio calculations with fast NNP predictions during the search. This procedure was applied to run the first NNP-powered reaction path network exploration using the AFIR method. We discovered that such explorations are particularly challenging for general purpose NNP models, and we identified the underlying limitations. In addition, we are proposing to overcome these challenges by complementing NNP models with fast semiempirical predictions. The proposed solution offers a generally applicable framework, laying the foundations to further accelerate ab initio kinetic studies with Machine Learning Force Fields, and ultimately explore larger systems that are currently inaccessible.
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Affiliation(s)
- Ruben Staub
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan
| | - Philippe Gantzer
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan
| | - Yu Harabuchi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan
- Japan Science and Technology Agency (JST), ERATO Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan
- Japan Science and Technology Agency (JST), ERATO Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
- Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan
| | - Alexandre Varnek
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan
- Laboratory of Chemoinformatics, UMR 7140, CNRS, University of Strasbourg, 67081 Strasbourg, France
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Tasi DA, Michaelsen T, Wester R, Czakó G. Quasi-classical trajectory study of the OH - + CH 3I reaction: theory meets experiment. Phys Chem Chem Phys 2023; 25:4005-4014. [PMID: 36649119 DOI: 10.1039/d2cp05553h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Regarding OH- + CH3I, several studies have focused on the dynamics of the reaction. Here, high-level quasi-classical trajectory simulations are carried out at four different collision energies on our recently developed potential energy surface. In all, more than half a million trajectories are performed, and for the first time, the detailed quasi-classical trajectory results are compared with the reanalysed crossed-beam ion imaging experiments. Concerning the previously reported direct dynamics study of OH- + CH3I, a better agreement can be obtained between the revised experiment and our novel theoretical results. Furthermore, in the present work, the benchmark geometries, frequencies and relative energies of the stationary points are also determined for the OH- + CH3I proton-abstraction channel along with the earlier characterized SN2 channel.
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Affiliation(s)
- Domonkos A Tasi
- Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Tim Michaelsen
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25/3, 6020 Innsbruck, Austria
| | - Roland Wester
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25/3, 6020 Innsbruck, Austria
| | - Gábor Czakó
- Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
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Murakami T, Matsumoto N, Takayanagi T, Fujihara T. The importance of nuclear dynamics in reaction mechanisms of acetylene cyclotrimerization catalyzed by Fe+-compounds. J Organomet Chem 2023. [DOI: 10.1016/j.jorganchem.2023.122643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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Tsutsumi T, Ono Y, Taketsugu T. Multi-state Energy Landscape for Photoreaction of Stilbene and Dimethyl-stilbene. J Chem Theory Comput 2022; 18:7483-7495. [PMID: 36351076 DOI: 10.1021/acs.jctc.2c00560] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have recently developed the reaction space projector (ReSPer) method, which constructs a reduced-dimensionality reaction space uniquely determined from reference reaction paths for a polyatomic molecular system and projects classical trajectories into the same reaction space. In this paper, we extend ReSPer to the analysis of photoreaction dynamics and relaxation processes of stilbene and present the concept of a "multi-state energy landscape," incorporating the ground- and excited-state reaction subspaces. The multi-state energy landscape successfully explains the previously established photoreaction processes of cis-stilbene, such as the cis-trans photoisomerization and photocyclization. In addition, we discuss the difference in the excited-state reaction dynamics between stilbene and 1,1'-dimethyl stilbene based on a common reaction subspace determined from the framework part of reference structures with different number of atoms. This approach allows us to target any molecule with a common framework, greatly expanding the applicability of the ReSPer analysis. The multi-state energy landscape provides fruitful insight into photochemical reactions, exploring the excited- and ground-state potential energy surfaces, as well as comprehensive reaction processes with nonradiative transitions between adiabatic states, within the stage of a reduced-dimensionality reaction space.
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Affiliation(s)
- Takuro Tsutsumi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo060-0810, Japan.,L-Station, Creative Research Institution (CRI), Hokkaido University, Sapporo060-0812, Japan
| | - Yuriko Ono
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo001-0021, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo001-0021, Japan
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Tsutsumi T, Ono Y, Taketsugu T. Reaction Space Projector (ReSPer) for Visualizing Dynamic Reaction Routes Based on Reduced-Dimension Space. Top Curr Chem (Cham) 2022; 380:19. [PMID: 35266073 DOI: 10.1007/s41061-022-00377-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 02/21/2022] [Indexed: 11/26/2022]
Abstract
To analyze chemical reaction dynamics based on a reaction path network, we have developed the "Reaction Space Projector" (ReSPer) method with the aid of the dimensionality reduction method. This program has two functions: the construction of a reduced-dimensionality reaction space from a molecular structure dataset, and the projection of dynamic trajectories into the low-dimensional reaction space. In this paper, we apply ReSPer to isomerization and bifurcation reactions of the Au5 cluster and succeed in analyzing dynamic reaction routes involved in multiple elementary reaction processes, constructing complicated networks (called "closed islands") of nuclear permutation-inversion (NPI) isomerization reactions, and elucidating dynamic behaviors in bifurcation reactions with reference to bundles of trajectories. Interestingly, in the second application, we find a correspondence between the contribution ratios in the ability to visualize and the symmetry of the morphology of closed islands. In addition, the third application suggests the existence of boundaries that determine the selectivity in bifurcation reactions, which was discussed in the phase space. The ReSPer program is a versatile and robust tool to clarify dynamic reaction mechanisms based on the reduced-dimensionality reaction space without prior knowledge of target reactions.
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Affiliation(s)
- Takuro Tsutsumi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yuriko Ono
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Tetsuya Taketsugu
- 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.
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