This paper presents a novel Chemist-AI Alignment framework for generating novel structures of quaternary ammonium compounds (QACs), a crucial class of antimicrobial agents.The framework uniquely integrates AI-driven small molecule generation with iterative feedback from chemist experts, leveraging both rapid assessments and comprehensive wet-lab validations to optimize for biological potency and synthetic feasibility.Central to the framework is a hierarchical generative model that captures the QAC hierarchical topology.Extensive experiments highlight the efficacy of the framework in identifying promising QAC candidates, many