arXiv:2608. 14076v1 Announce Type: cross Abstract: Transition-state (TS) structures define the energetic barriers and mechanistic pathways of elementary chemical reactions, yet their identification remains computationally demanding because conventional saddle-point searches require expensive quantum-mechanical calculations.
By Kaipeng Zeng, Wenxi Zhai, Shengrui Xu, Jie Zhao, Bowen Li, Shiyue Wang, Junchi Yan, Tong Zhu
MAELLE is a mechanistic reaction prediction framework that models chemical reactions as discrete flow matching over graph-structured electron occupation vectors. It formulates the reactant-to-product mapping as a Continuous-time Markov Chain on electron sites and uses Optimal Transport to generate mechanistically interpretable edit trajectories without elementary step annotations. The method achieves competitive accuracy on the USPTO-480K benchmark, remains robust in out-of-distribution scenarios, and can recover mechanistic pathways that align with known chemistry and predict side products.
By Nguyen Xuan-Vu, Octavian Susanu, Daniel Armstrong, Philippe Schwaller
arXiv:2602. 13136v2 Announce Type: replace Abstract: Template-free retrosynthesis methods treat the task as black-box sequence generation, limiting learning efficiency, while semi-template approaches rely on rigid reaction libraries that constrain generalization.
By Chenguang Wang, Zihan Zhou, Lei Bai, Tianshu Yu
The paper introduces GenAIMMD, an iterative algorithm that learns the committor function and trains a conditioned Boltzmann Generator to generate uncorrelated transition paths without prior knowledge of the reaction coordinate. This method combines transition path sampling with committor learning, enabling fully parallelizable sampling. Benchmarks on a toy model and a polymer system show a substantial performance improvement over standard TPS.
By Maximilian Negedly, Sebastian Falkner, Alessandro Coretti, Christoph Dellago
arXiv:2610.32602v1 Announce Type: new
Abstract: The natural units of structured discrete generation are often not independent single-component edits but richer actions: attaching a fragment to a mole...
By Niklas Kemper, Marten Lienen, David L\"udke, Stephan G\"unnemann
Studying the dynamical behavior of a system often depends on characterizing how it transitions between long-lived states. Because such transitions are rare, observing them usually requires specialized...