Rate Constant Matrix Contraction Method for Systematic Analysis of Reaction Path Networks

Sumiya, Yosuke; Maeda, Satoshi

doi:10.1246/cl.200092

Cited by 44 publications

(70 citation statements)

References 66 publications

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“…Details of the SC-AFIR method and the traffic volume index are described in previous work. 9,16 Data science method…”

Section: Methodsmentioning

confidence: 99%

“…[3][4][5][6][7] In general, chemical kinetics is coupled with a calculated chemical reaction network in order to determine the reaction pathway. 8,9 However, one can consider that hidden trends and patterns for identifying the reaction path within the chemical reaction network should be present, considering that the energy landscape created by rst principles calculation follows certain rules. In view of how a chemical reaction network is formed, the network can be treated as a graph data structure.…”

Section: Introductionmentioning

confidence: 99%

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Mining hydroformylation in complex reaction networkviagraph theory

Takahashi

Maeda

2021

RSC Adv.

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“…Details of the SC-AFIR method and the traffic volume index are described in previous work. 9,16 Data science method…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Mining hydroformylation in complex reaction networkviagraph theory

Takahashi

Maeda

2021

RSC Adv.

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“…The kinetics-based navigation option, which ranks MINs based on their kinetic importance and avoids path searching from those of low rank, was used. 34 Obtained force-induced paths were re-optimized by using the locally updated planes (LUP) method. 40,41 The LUP method optimizes discrete path points toward the direction perpendicular to path tangent and gives a LUP path which can be a good approximation of the corresponding F I G U R E 1 Initial structure of the reaction path search.…”

Section: Making a Reaction Route Network Of Ch 3 Oh Decomposition Reaction On A Pt(111) Surfacementioning

confidence: 99%

“…Then, the resulted network was kinetically analyzed by applying the rate constant matrix contraction (RCMC) method. 33,34 The approach that utilizes AFIR and RCMC methods and elucidates the reaction mechanism through kinetic analysis of the reaction route network, has been applied to two simple reactions: water generation on Cu(111) surface 26 and CO oxidation on Pt(111) surface. 27 In this article, the reaction route network of the methanol decomposition reaction on a Pt(111) surface is presented.…”

Section: Introductionmentioning

confidence: 99%

A reaction route network for methanol decomposition on a Pt(111) surface

2021

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A reaction route network for the decomposition reaction of methanol on a Pt(111) surface was constructed by using the artificial force-induced reaction (AFIR) method, which can search for reaction paths automatically and systematically. Then, the network was kinetically analyzed by applying the rate constant matrix contraction (RCMC) method. Specifically, the time hierarchy of the network, the time evolution of the population initially given to CH 3 OH to the other species on the network, and the most favorable route from CH 3 OH to major and minor products were investigated by the RCMC method. Consistently to previous studies, the major product on the network was CO+4H, and the most favorable route proceeded through the following steps: CH 3 OH ! CH 2 OH+H ! HCOH+2H ! HCO+3H ! CO+4H. Furthermore, paths to byproducts found on the network and their kinetic importance were discussed. The present procedure combining AFIR and RCMC was thus successful in explaining the title reaction without using any information on its product or the reaction mechanism.

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“…Data used to illustrate the functionality of RePathDB were taken from reference 33 , and are available from the authors on demand.…”

Section: Code Availabilitymentioning

confidence: 99%

Combined Graph/Relational Database Management System for Calculated Chemical Reaction Pathway Data

Gimadiev

Nugmanov

Batyrshin

et al. 2021

J. Chem. Inf. Model.

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Nowadays quantum chemical calculations are widely used to generate extensive datasets for machine learning applications, however, generally these sets only include information on equilibrium structures and some close conformers. Exploration of potential energy surface provides an important information on ground and transition states, but analysis of such data is complicated due to the number of possible reaction pathways. Here, we present RePathDB, a database system for managing 3D structural data for both ground and transition states resulted from quantum chemical calculations. Our tool allows to store, to assemble and to analyze reaction pathway data. It combines relational database CGR DB for handling compounds and reactions as molecular graphs with a graph database architecture for the pathway analysis by graph algorithms. Original Condensed Graph of Reaction Technology is used to store any chemical reaction as a single graph.

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Rate Constant Matrix Contraction Method for Systematic Analysis of Reaction Path Networks

Cited by 44 publications

References 66 publications

Mining hydroformylation in complex reaction networkviagraph theory

Mining hydroformylation in complex reaction networkviagraph theory

A reaction route network for methanol decomposition on a Pt(111) surface

Combined Graph/Relational Database Management System for Calculated Chemical Reaction Pathway Data

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