Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization. Mechanistically explaining these relationships requires interpreting structural evidence through scientific principles and physical constraints, from stereochemistry and bonding to symmetry, energetics and periodic order.
arXiv:2605. 02937v2 Announce Type: replace-cross Abstract: Deep learning in de novo protein design has achieved atomic-level fidelity.
By Fang Wu, Weihao Xuan, Heli Qi, Hanqun Cao, Heng-Jui Chang, Zeqi Zhou, Haokai Zhao, Ma Jian, Carl Ma, Yu-Chi Cheng, Kuan Pang, Xiangru Tang, Zehong Wang, Guanlue Li, Hanchen Wang, Kejun Ying, Pan Lu, Chiho Im, Seungju Han, Peng Xia, Tinson Xu, Yinxi Li, Deyao Zhu, Pheng-Ann Heng, Naoto Yokoya, Masashi Sugiyama, Li Erran Li, Jure Leskovec, Yejin Choi
arXiv:2605. 01625v3 Announce Type: replace Abstract: Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology.
By Viet Thanh Duy Nguyen, John K. Johnstone, Truong-Son Hy
The paper introduces a multitask large reasoning model for molecular science that incorporates chemical knowledge via a multispecialist architecture, chain-of-thought supervision, and molecule-informed reinforcement learning. It coordinates prediction and inference specialists across ten molecular tasks—including description, generation, nomenclature translation, property prediction, and reaction prediction—using task-conditioned routing. The model surpasses more than 20 general-purpose and molecular large language models, improving aggregate performance by 50.3% and outperforming leading multitask baselines on most tasks, while maintaining interpretable chemical inference and demonstrating a workflow for CNS candidate generation and retrosynthetic planning.
By Pengfei Liu, Shuang Ge, Xiaobo Wang, Xin Liu, Jun Tao, Yan Li, Chao Liu, Ling Chen, Zhixiang Ren
arXiv:2606. 07712v1 Announce Type: cross Abstract: Progress in AI-driven crystal materials science has so far been carried by narrow architectures purpose-built for individual tasks -- graph neural networks for property prediction, diffusion and flow-matching models for crystal generation -- each excelling within its niche yet unable to act as a shared backbone across the full spectrum of materials problems.
By Zhan'ao Yao, Boxuan Zhang, Jingyuan Shu, Xiaoyu Wu, Rongyan Wang, Linjing Li, Dajun Zeng, Yudong Yao, Tingwei Chen, Youwei Wang, Xiaolin Zhao, Jiahui Shi, Jianjun Liu
ChemVTS-Bench is a domain-authentic benchmark that evaluates Visual‑Textual‑Symbolic reasoning in multimodal large language models for chemistry. It presents diverse chemical problems—organic molecules, inorganic materials, and 3D crystal structures—in three input modes: visual-only, visual‑text hybrid, and SMILES-based symbolic. The benchmark includes an automated agent workflow for inference, answer verification, and failure diagnosis, and shows that visual-only inputs and structural chemistry remain challenging for current models.
By Zhiyuan Huang, Baichuan Yang, Zikun He, Yanhong Wu, Fang Hongyu, Zhenhe Liu, Lin Dongsheng, Bing Su
arXiv:2606. 30961v1 Announce Type: cross Abstract: Advances in deep learning architectures and representations have enabled ML-driven chemical property prediction, but state-of-the-art (SOTA) models have remained largely confined to independent codebases and lack support for diverse chemical species.
By Jacob W. Toney, Samir Darouich, Yiran Wang, Aaron G. Garrison, Johannes K\"astner, Heather J. Kulik
arXiv:2606. 03057v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly used for molecular tasks, but it remains unclear which molecular representation to use.
By Arun Raja, Garrett M. Morris, Kian Ming A. Chai
arXiv:2602. 02320v4 Announce Type: replace-cross Abstract: Molecular function is largely determined by structure.
By Feiyang Cai, Guijuan He, Yi Hu, Jingjing Wang, Joshua Luo, Tianyu Zhu, Srikanth Pilla, Gang Li, Ling Liu, Feng Luo
ReactBench is a benchmark designed to evaluate the structural reasoning abilities of multimodal large language models (MLLMs) using chemical reaction diagrams. The dataset contains 1,618 expert‑annotated question‑answer pairs that test reasoning across four hierarchical task dimensions, from simple endpoint counting to complex topological analysis. Evaluation of 24 MLLMs shows a performance gap of more than 30% between anchor‑based tasks and holistic structural reasoning tasks, indicating that current models struggle with reasoning over branching, converging, and cyclic structures.
By Qiang Xu, Shengyuan Bai, Yu Wang, He Cao, Leqing Chen, Yuanyuan Liu, Bin Feng, Zijing Liu, Yu Li
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
oMeBench is a large-scale, expert-curated benchmark designed to evaluate large language models (LLMs) on organic mechanism reasoning. It contains over 10,000 annotated mechanistic steps, including reaction type labels, intermediate structures, and difficulty ratings, and introduces the oMeS scoring framework to assess logical consistency and chemical structural similarity. Evaluation shows that while current LLMs display promising chemical intuition, they often fail to produce correct and consistent multi-step reasoning, though prompting and fine-tuning can bring smaller models up to the level of closed‑source frontier models.
By Ruiling Xu, Yifan Zhang