Principal Scientist, Synthetic & Discovery Chemistry Merck KGaA - 3.8 Billerica, MA Job Details $140,000 - $190,000 a year 1 hour ago Benefits Health insurance Paid time off Opportunities for advancement Qualifications Doctor of Philosophy Handling small molecules Automated liquid handling systems Cross-functional communication Nuclear magnetic resonance (NMR) spectroscopy Full Job Description Work Your Magic with us! Ready to explore, break barriers, and discover more? We know you've got big plans - so do we! Our colleagues across the globe love innovating with science and technology to enrich people's lives with our solutions in Healthcare, Life Science, and Electronics. Together, we dream big and are passionate about caring for our rich mix of people, customers, patients, and planet. That's why we are always looking for curious minds that see themselves imagining the unimaginable with us. United As One for Patients, our purpose in Healthcare is to help create, improve and prolong lives. We develop medicines, intelligent devices and innovative technologies in therapeutic areas such as Oncology, Neurology and Fertility. Our teams work together across 6 continents with passion and relentless curiosity in order to help patients at every stage of life. Joining our Healthcare team is becoming part of a diverse, inclusive and flexible working culture, presenting great opportunities for personal development and career advancement across the globe. About 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. Your Role 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 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 Responsibilities Synthesis planning and execution 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. External customer chemistry support 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. Team contribution and junior chemist mentorship 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.

Who You Are:

Minimum 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. Preferred Requirements 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. What We Offer A 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. Location This 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-$190,000 The 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 .

What we offer:

We are curious minds that come from a broad range of backgrounds, perspectives, and life experiences. We believe that this variety drives excellence and innovation, strengthening our ability to lead in science and technology. We are committed to creating access and opportunities for all to develop and grow at your own pace. Join us in building a culture of inclusion and belonging that impacts millions and empowers everyone to work their magic and champion human progress! Apply now and become a part of a team that is dedicated to Sparking Discovery and Elevating Humanity!