Principal Scientist, Synthetic & Discovery Chemistry

About AIDDAI & 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.Your RoleWe 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 plan and execute single- and multi-step routes optimized for automation, and 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.Key ResponsibilitiesSynthesis planning and executionPlan 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.External customer chemistry supportAct 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.Team contribution and junior chemist mentorshipSupervise 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.Who You Are: Minimum QualificationsPhD 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.Preferred RequirementsExperience 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.What We OfferA role at the chemistry heart of a first-in-class autonomous drug discovery platform -- your synthesis decisions directly drive what MLOOP learns.A highly collaborative, interdisciplinary team of scientists, automation engineers, and data scientists operating at the frontier of AI-driven discovery.Broad chemistry scope: library design, multi-step synthesis, customer programs, and automation integration -- no two weeks look the same.LocationThis is a fully onsite role required to be site based in our Billerica, MA facility. We do offer a hybrid flexible work arrangement. Travel is expected to be limited and mainly related to partner and customer engagements.Pay Range: $140,000-$190,000The offer range represents the anticipated low and high end of the base pay compensation for this position. The actual compensation offered will be determined by factors such as location, level of experience, education, skills, and other job-related factors. Position may be eligible for sales or performance-based bonuses. Benefits offered by the Company include health insurance, paid time off (PTO), retirement contributions, and other perquisites. For more information click here.