Early-stage molecular design is an iterative process, not just a task of generating molecules. Researchers turn broad goals into design strategies, refine candidates, assess many properties, and gather evidence before synthesis and tests. AI methods can generate molecules, optimize several goals, predict properties, dock compounds, and account for synthesis. Yet these functions are spread across specialized tools. Experts must still coordinate each step, judge interim results, and integrate evidence. The central challenge is thus to turn research intent into adaptive, traceable runs grounded in scientific tools. We cast this challenge as intent-to-evidence molecular design workflow execution and present CAi Copilot, an expert-oriented agent with three linked layers. The Research Interface Layer turns intent into an executable plan. The Agent Reasoning Layer uses interim results to guide each run. The Execution Substrate supplies molecular tools, metrics, reusable utilities, and backend services. Across 45 tasks, CAi achieves the strongest overall performance, with an outcome score of 84.59, exceeding the next-best result by 18.07 points. Additional benchmarks test how CAi coordinates generation, screening, and multi-criteria evaluation, while exposing limits in long-horizon execution. These results show that CAi turns broad molecular-design intent into transparent, traceable workflows that connect interim decisions to candidate-level evidence.
Large language model (LLM) agents have been increasingly adopted in scientific research for organizing and invoking specialized computational tools. However, their reliance on predefined tool spaces with static semantics limits their applicability to open-world scientific workflows, where tool requirements, capabilities, and boundaries evolve dynamically. To this end, we propose SciToolAgent-Evo, an ontology-aware self-evolving agent for open-world scientific tool acquisition. Driven by an evolving memory of skills, experiences, and an ontologized tool graph, it distills generalizable knowledge from contrastive trajectories during accumulation, whereas during inference, it formulates active requests and utilizes a LinUCB-based bandit gate to dynamically balance exploration and exploitation. Once a novel tool is acquired, its scientific ontology is completed online for seamless integration into the known graph. Moreover, we introduce OpenSciToolBench, a benchmark containing 900 realistic tasks across four difficulty levels. Extensive evaluations show that SciToolAgent-Evo achieves state-of-the-art performance, validating its robustness and generalization.