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 make-and-test lab, automated synthesis, analytical characterization, and biological readout come together to accelerate discovery.
Your RoleWe are hiring a Senior Scientist, Synthetic Chemistry, to add independent synthetic organic chemistry expertise to our Billerica lab. This is a hands-on bench role. You will make molecules: building blocks, intermediates, reference compounds and target compounds that our automated platform, our biology assays and our AI models depend on. You will own your chemistry from route to characterized compound, you will help build our Direct-to-Biology (D2B) workflow, in which compounds move from plate-based synthesis straight into biological assays, and you will help validate the reaction classes that run on our automated platform by generating the manual reference data, substrate sets and failure analysis that make automation trustworthy.
Reporting to the Head of Science Operations, you will work alongside our synthetic and discovery chemistry lead, our chemistry automation team, and colleagues in Automation Engineering, Biology, and Data Science. Automation experience is welcome but not required. Strong, independent, well-documented synthetic chemistry is.
Key ResponsibilitiesSynthesis and compound supply- Design and execute multi-step syntheses of small molecules, building blocks and intermediates, independently and to agreed timelines.
- Resynthesize and scale up compounds of interest for biological and ADME testing, including route scouting when the original route does not scale.
- Prepare reference compounds and substrate sets that support reaction-class validation on the automated platform.
Direct-to-Biology (D2B) chemistry- Develop and run plate-based, low-volume synthesis whose crude or minimally purified products can be dosed directly into biological assays.
- Select reaction classes, reagents, solvents and workups that are compatible with downstream assays, and quantify conversion and purity well enough to interpret the biological readout.
- Work with medicinal chemistry automation, automation engineering and biology colleagues to make the D2B workflow robust, automated and repeatable, including plate layouts, liquid handling and sample handoff to assays.
- Confirm D2B hits by resynthesis and purification, and feed the comparison between crude and purified results back into the workflow.
Reaction validation and method development- Run manual reference reactions and condition screens alongside automated runs, so that platform results can be benchmarked and failures diagnosed.
- Develop and improve synthetic, workup and purification methods; report results quantitatively, including yield, purity and reproducibility.
- Work with the chemistry automation team to translate robust bench procedures into automation-ready protocols.
Purification and characterization- Purify compounds by automated and manual chromatography, including reverse phase where needed.
- Characterize compounds by 1D and 2D NMR, HPLC or UPLC, and LC-MS; interpret data independently and flag ambiguity rather than resolving it silently.
Data quality and datasets for machine learning- Record complete experimental detail in the ELN, including failed and partial results, with metadata that downstream AI and ML users can rely on.
- Contribute to plate-based and library chemistry that produces balanced, model-ready datasets.
Lab operations, safety and team- Work to a high safety standard; follow and help maintain SOPs and chemical inventory practices.
- Mentor research associates, contractors and interns in synthetic technique and record-keeping.
- Present results clearly to chemistry, automation, biology and data science colleagues.
Who You Are: Minimum Qualifications- PhD in Organic, Synthetic or Medicinal Chemistry, or a closely related field, with at least 1 year of post-PhD synthetic chemistry experience in industry or an equivalent research setting; or MS with 5+ years; or BS with 8+ years of hands-on synthetic chemistry.
- Demonstrated independent capability in multi-step organic synthesis, including reaction design, setup, workup, air-free technique and purification by flash chromatography.
- Strong structural characterization and purity assessment by 1D and 2D NMR, HPLC or UPLC, and LC-MS, with independent spectral interpretation.
- Evidence of having developed or measurably improved a synthetic, purification or analytical method.
- Meticulous, complete and honest experimental record-keeping, including negative results.
- Willingness to work hands-on at the bench daily in a fully on-site laboratory role.
Preferred Requirements- Experience with library synthesis, parallel chemistry or high-throughput experimentation, particularly where data were used to train or validate machine learning models.
- Hands-on experience with Direct-to-Biology, nanomole-scale or plate-based synthesis coupled directly to biological assays.
- Hands-on experience with automated synthesis, automated purification or robotic liquid handling.
- Experience with common medicinal chemistry reaction classes across substrate scope, for example amide couplings, reductive aminations, cross-couplings and protecting-group chemistry.
- Scale-up of a synthetic route or purification process from milligram to multigram scale.
- Analytical breadth beyond the core: GC-MS, UPLC-ELSD, FPLC, MALDI, IR or UV-vis.
- Experience with ELN or LIMS systems and an understanding of why data lineage matters.
- Experience across modalities, for example lipids and delivery chemistry, conjugates, PROTACs or molecular glues.
What We Offer- Independent ownership of synthetic chemistry in a lab where every compound you make feeds AI-driven design and an automated discovery platform.
- A central role in building Direct-to-Biology, one of the capabilities that closes our loop from design to biological readout.
- Exposure to and training on automated synthesis, with a path toward reaction-class ownership if that is where you want to grow.
- A highly collaborative, interdisciplinary team spanning chemistry, biology, automation engineering, software and data science.
LocationThis is a fully onsite role required to be site based in our Billerica, MA facility.
Pay Range: $85,000-$110,000
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.
