Although LLM-based agents are proven to master tool orchestration in scientific fields, particularly chemistry, their single-task performance remains limited by underlying tool constraints. To this end, we propose tool amplification, a novel paradigm that enhances the collective capabilities of specialized tools through optimized, dynamic coordination within individual tasks. Instantiating this paradigm, we introduce ChemAmp, a computationally lightweight framework that dynamically treats chemistry tools (e.g., UniMol2, Chemformer) as composable building-block agents. It constructs task-specialized super-agents that transcend atomic tool constraints with limited data ($\leq$10 samples). Our evaluations across four core chemistry tasks molecular design, molecule captioning, reaction prediction, and property prediction demonstrate that ChemAmp outperforms chemistry-specialized models, generalist LLMs, and agent systems with tool orchestration. Critically, this bottom-up construction strategy enables 94\% inference token cost reductions versus vanilla multi-agent systems.