Principal Scientist, Synthetic & Discovery Chemistry

About the role

AIDD AI & Automation in Drug Discovery (AIDD) at EMD is building and scaling AI-driven and automated discovery capabilities. We connect machine learning, computational science, and lab automation to enable closed-loop chemistry and biology experimentation and faster, higher-quality scientific decisions. In our Boston-area autonomous make-and-test lab, automated synthesis, analytical characterization, and biological readout come together to accelerate discovery.

We are hiring a Principal Scientist in Synthetic & Discovery Chemistry to own our small molecule chemistry design and execution capabilities within the closed-loop discovery engine. What we need is deep synthetic expertise: strong chemical synthetic knowledge to plan and execute single- and multi-step routes optimized for automation, and to drive chemistry strategy in a high-throughput, data-rich environment. Reporting to the Head of Science Operations, you will collaborate closely with our Automation, Biology, and Data Science teams to ensure chemistry output is fast, high quality, and machine-learning ready. You will also serve as the chemistry subject matter expert for selected external customer programs, translating scientific requirements into executable synthesis plans.

Responsibilities

• Plan and execute single- and multi-step synthetic chemistry workflows within the AIDD automated lab; collaborate with Automation Engineers to make routes robot-executable and throughput-compatible.
• Troubleshoot chemistry, optimize reaction conditions, and maintain high data quality across synthesis campaigns.
• Own NMR and analytical data workflows; ensure accurate compound characterization and data integrity in ELN and data systems.
• Develop multi-step synthesis concepts (2-3 steps) and translate them into enumerable, automatable routes.
• Act as chemistry subject matter expert for selected external customer programs; collaborate with BD and project leads to define chemistry scope, design compound sets, and meet customer milestones.
• Represent AIDD chemistry capabilities credibly in partner and customer interactions.
• Supervise and mentor junior chemists and contractors; ensure high execution standards and lab safety compliance.
• Contribute to SOPs, chemistry best practices, and continuous improvement of lab workflows.

Qualifications

• PhD in Organic Chemistry, Medicinal Chemistry, Chemical Biology, or a closely related field.
• At least 5 years of industry experience in pharmaceutical, biotech, or related synthetic chemistry.
• Strong track record in synthetic organic chemistry, with hands-on experience in parallel synthesis.
• Experience working in or alongside automated chemistry platforms (high-throughput synthesis, liquid handling, or similar); comfort translating bench routes into automation-compatible protocols.
• Proficiency in NMR and standard small molecule analytical characterization.
• Proven ability to work in cross-functional teams with biologists, automation engineers, and data scientists.

Skills

• Experience with diversity-oriented or combinatorial synthesis; familiarity with commercial building block databases (e.g., Enamine, ChemDiv, Mcule) and enumeration workflows.
• Familiarity with AI- or ML-augment