Chemography‐guided analysis of a reaction path network for ethylene hydrogenation with a model Wilkinson's catalyst

• Published in: Molecular informatics Vol. 44; no. 1; pp. e202400063 - n/a
• Main Authors: Gantzer, Philippe, Staub, Ruben, Harabuchi, Yu, Maeda, Satoshi, Varnek, Alexandre
• Format: Journal Article
• Language: English
• Published: Germany Wiley Subscription Services, Inc 01.01.2025; Wiley-VCH
• Subjects: Algorithms; artificial force induced reaction; Atomic structure; Cartography; Catalysis; Catalysts; Chemical reactions; Chemical Sciences; Cheminformatics; Density functional theory; Ethylenes - chemistry; generative topographic mapping; Hydrogenation; neural network potential; Neural networks; Neural Networks, Computer; Permutations; Potential energy; Topographic mapping; neural network potential; artificial force induced reaction; generative topographic mapping
• ISSN: 1868-1743; 1868-1751; 1868-1751
• DOI: 10.1002/minf.202400063

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.