Generative Model for Constructing Reaction Path from Initial to Final States

Abstract

Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths can be difficult for humans. This paper presents an innovative approach that utilizes neural networks to generate initial guesses for reaction pathways based on the initial state and learning from a database of low-energy transition paths. The proposed method is initiated by inputting the coordinates of the initial state, followed by progressive alterations to its structure. This iterative process culminates in the generation of the guess reaction path and the coordinates of the final state. The method does not require one-the-fly computation of the actual potential energy surface, and is therefore fast-acting. The application of this geometry-based method extends to complex reaction pathways illustrated by organic reactions. Training was executed on the Transition1x dataset of organic reaction pathways. The results revealed the generation of reactions that bore substantial similarities with the test set of chemical reaction paths. The method's flexibility allows for reactions to be generated either to conform to predetermined conditions or in a randomized manner.