Principal Scientist, Synthetic & Discovery Chemistry

Merck•Billerica, MA

6d•Onsite

About The Position

The AI & Automation in Drug Discovery (AIDD) team 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. This role is for a Principal Scientist in Synthetic & Discovery Chemistry to own small molecule chemistry design and execution capabilities within the closed-loop discovery engine. The ideal candidate will have deep synthetic expertise, strong chemical synthetic knowledge, and the ability to plan and execute single- and multi-step routes optimized for automation, driving chemistry strategy in a high-throughput, data-rich environment. Reporting to the Head of Science Operations, this role involves close collaboration with Automation, Biology, and Data Science teams to ensure chemistry output is fast, high quality, and machine-learning ready. The scientist will also serve as the chemistry subject matter expert for selected external customer programs, translating scientific requirements into executable synthesis plans.

Requirements

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

Nice To Haves

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-augmented experimental design; comfort interpreting model outputs to guide synthesis prioritization
Experience with ELN systems and data-driven chemistry workflows in a high-throughput setting
Background in small molecule drug discovery programs (oncology, genetic disease, or similar) with exposure to early-stage hit identification and compound set design
Experience managing or coordinating with CRO or external chemistry partners
Comfort with pharmaceutical synthesis beyond classic MedChem -- process chemistry mindset, route scouting, yield and purity optimization at small scale

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.