cs.AIAug 7, 2025

Large Language Models Transform Organic Synthesis From Reaction Prediction to Automation

Authors: Kartar Kumar, Rajesh Kumar, Nikesh Lagun

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Abstract

Large language models (LLMs) are beginning to reshape how organic-synthesis workflows are represented, queried, planned, and connected to experimental automation. Assessing their contribution is not straightforward because reaction-specific transformers, chemistry-adapted LLMs, tool-using agents, optimizers, and autonomous laboratories are often discussed under the same broad terminology despite operating at different levels of the synthesis workflow. This Review traces the progression from reaction prediction and retrosynthetic planning to reaction development, literature-to-protocol translation, and robotic execution, with representative numerical claims verified against primary sources available through 4 September 2026. We examine where language models provide genuine added value, where established specialist methods remain the principal source of performance, and how retrieval, uncertainty-aware optimization, deterministic chemistry tools, robotics, sensing, and human oversight alter system behavior. The evidence shows a clear transition from isolated language-model demonstrations toward modular scientific systems that combine broad language priors with specialized computation and experimentally grounded feedback. Emerging work on multimodal reaction understanding, standardized tool interoperability, provenance-aware execution, and programmable laboratory infrastructure extends this transition further. Despite this progress, reliable deployment continues to depend on generalization beyond historical reaction corpora, calibrated uncertainty, transparent component attribution, safety controls, reproducible system state, and prospective experimental validation.

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