Organic Chemistry as a Catalyst for AI Innovation: Challenges, Methods, and Emerging Paradigms

Artificial intelligence and organic chemistry are redefining each other in a fundamentally bidirectional relationship. This Review highlights how the intrinsic challenges of organic chemistry have acted as a catalyst for conceptual and methodological innovation in AI itself. Sparse and heterogeneous reaction data sets spurred the development of self-supervised and few-shot learning paradigms; the combinatorial complexity of multireactant chemistry motivated the transition from graph neural networks to hypergraph architectures; the need to bridge symbolic chemical reasoning with statistical prediction inspired chemical language models grounded in large language model frameworks; and the iterative, decision-intensive nature of synthesis planning catalyzed the rise of autonomous agentic systems. We survey the multimodal landscape of chemical data, tracing the evolution of molecular representations from classical fingerprints to geometric encodings and examining how each representation class shapes downstream model capabilities. We analyze how data scarcity and uneven property distributions have driven advances in transfer learning, self-supervised pretraining, and meta-learning frameworks tailored to molecules and reactions. Reaction prediction, mechanistic inference, and retrosynthesis planning are examined as core areas where chemistry has shaped modern AI techniques. We further explore chemical reasoning through multimodal fusion, generative molecular design, and self-driving laboratories. We conclude by identifying persistent challenges, including data sparsity, selection bias, benchmark-to-lab gaps, and reproducibility.