ChemBART is a BART‑based language model trained on holistic reaction expressions (Reactant > Reagent > Product) using a mask‑filling objective. It can solve diverse chemical tasks such as precursor/reagent generation, temperature‑yield regression, and property classification, and it is integrated with Monte Carlo tree search to design multi‑step synthesis routes. The model’s predictions were experimentally validated, yielding shorter synthetic pathways with over 20 % higher yield than literature benchmarks.
By Kenan Li, Yijian Zhang, Jin Wang, Haipeng Gan, Zeying Sun, Xiaoguang Lei, Hao Dong
arXiv:2604.07669v3 Announce Type: replace-cross
Abstract: Synthesizable molecular optimization seeks to improve target properties while ensuring that molecular modifications follow feasible synthetic...
By Tao Li, Kaiyuan Hou, Tuan Vinh, Fanglei Xue, Monika Raj, Zhichun Guo, Carl Yang
The paper introduces Align-React, a chemical reaction representation learning framework that incorporates atomic correspondence between reactants and products, an adapter for embedding reaction conditions, and a Reaction-Center-Aware attention mechanism. These components enable the model to capture precise molecular transformations and focus on critical functional groups, leading to improved performance across a variety of organic reaction tasks. The framework outperforms existing architectures on most benchmark datasets.
By Kaipeng Zeng, Xianbin Liu, Yu Zhang, Xiaokang Yang, Yaohui Jin, Yanyan Xu
The paper introduces Top‑K prompting as a training and inference strategy to better capture the diverse, plausible predictions inherent in single‑step retrosynthesis. Using an ultra‑large dataset (CREED‑CCV‑2+USPTO‑XL) of ~45.6 million verified reactions, the authors train the Chemistry Constraint‑Consistent Language Model (C3LM). With fine‑tuning that incorporates ChemCensor‑based and novelty‑oriented rewards, C3LM achieves state‑of‑the‑art performance on the OOD URSA‑expert‑2026 benchmark and demonstrates complementary reaction space exploration compared to conventional models, suggesting benefits for ensemble‑based retrosynthesis systems.
By Bogdan Zagribelnyy, Ivan Ilin, Nikita Bondarev, Maksim Kuznetsov, Mathieu Reymond, Vladimir Aladinskiy, Alex Aliper, Alex Zhavoronkov
RxnOptBench is a new benchmark that tests large language models on the task of selecting optimal reaction conditions—such as catalyst, ligand, solvent, temperature, and atmosphere—by reading real condition‑screening tables from 2025 organic‑methodology papers. The benchmark uses a continuous relative score that combines yield with stereochemical metrics (ee, dr, rr) and includes a design that separates in‑context literature use from mere memorization. Evaluation across nine frontier LLMs and three chemistry‑specialized LLMs shows that even the best models still have significant room for improvement, with chemistry‑specialized models performing at random levels on multi‑axis selection while open‑weight models approach proprietary models.
By Lingli Ge, Yubin Wang, Junyuan Gao, Jiahe Song, Jiaxing Sun, Boyu Zhu, Haote Yang, Jingchao Wang, Lixin Ma, Jiang Wu, Yuqiang Li, Conghui He
arXiv:2607. 12771v1 Announce Type: new Abstract: Reaction mechanisms consist of the step-by-step sequences of elementary reactions that explain chemical transformations.
By Xingyu Dang, Haocheng Tang, Junmei Wang, Yanjun Li
arXiv:2606. 11256v1 Announce Type: cross Abstract: Designing molecules with target properties is most useful when candidate structures are accompanied by feasible synthetic routes.
By C\'esar Ojeda, Darius A. Faroughy, Maryam Karimi, Payam Zarrintaj, Mir Mehdi Seyedebrahimi, Mart\'in Carballo-Pacheco
The paper introduces ChemDiffAgent, a masked diffusion language agent designed for tool‑integrated chemical reasoning. Unlike traditional autoregressive agents, it treats reasoning as iterative denoising over interleaved reasoning and tool‑use trajectories, allowing joint decision making under full‑trajectory context. A two‑stage post‑training framework further refines tool use and reasoning, and the authors benchmark the model on six chemistry tasks, reporting a ~20% performance gain over autoregressive baselines and competitive results against larger models.
By Mengdi Liu, Chenghao Jia, Hong Chang, Shiguang Shan
arXiv:2607. 08003v1 Announce Type: cross Abstract: Catalysts are essential for sustainable chemical manufacturing, yet discovering novel architectures remains a bottleneck dominated by trial-and-error experimentation and computationally intensive screening.
By Sutanay Choudhury, Anwesha Banerjee, Udishnu Sanyal, Jorin Dawidowicz, Chiezugolum Ijeoma Odilinye, Jesun Firoz, Liney Arnadottir, Simone Raugei, Johannes Lercher, Arnab Dutta
arXiv:2502. 18966v2 Announce Type: replace Abstract: General chemical reaction conditions that achieve consistently high performance across multiple substrates are important for practical applications such as library synthesis and high-throughput experimentation.
By Stefan P. Schmid, Ella Miray Rajaonson, Cher Tian Ser, Mohammad Haddadnia, Shi Xuan Leong, Al\'an Aspuru-Guzik, Agustinus Kristiadi, Kjell Jorner, Felix Strieth-Kalthoff
The paper reports a large-scale, compute-controlled study of Chemical Language Models (CLMs) involving over 30,000 experiments across different molecular representations, tokenizations, model sizes, datasets, and architectures. It finds clear scaling trends in pretraining loss but shows that these improvements do not translate into proportional gains in goal-directed molecular design, with chemical syntax saturating early while semantic properties develop more slowly. The authors release a new suite of models, NovoMolGen, that achieves state-of-the-art results in drug discovery tasks, highlighting a disconnect between representation learning and downstream design and calling for new pretraining paradigms that target chemical semantics.
By Roshan Balaji, Kamran Chitsaz, Quentin Fournier, Nirav Pravinbhai Bhatt, Sarath Chandar
arXiv:2606. 17445v1 Announce Type: new Abstract: Inverse design of heterogeneous catalysts remains challenging because catalyst surfaces exhibit substantial structural complexity with coupled surface-adsorbate interactions across a vast chemical space that is difficult to explore efficiently through conventional screening alone.
By Dong Hyeon Mok, Jonggeol Na, Seoin Back