Computational Synthetic Chemist

Our mission is to make biology easier to engineer. Ginkgo is constructing, editing, and redesigning the living world in order to answer the globe’s growing challenges in health, energy, food, materials, and more. Our bioengineers make use of an in-house automated foundry for designing and building new organisms.

Boston, Massachusetts

Ginkgo Data points, a business unit within Ginkgo Bioworks, is ushering in the coming era of AI-backed biotechnology breakthroughs. By leveraging Ginkgo’s automation and digital infrastructure, Data points builds high-quality, large-scale datasets and technical capabilities that accelerate drug discovery and development.

The Small Molecules team is looking for a synthetic organic chemist to support computationally enabled synthetic chemistry. This role sits between the high-throughput and direct-to-biology core and the cheminformatics function, connecting route design, practical synthesis, reaction prediction, automated experimentation, and structured data capture.

We are hiring a Senior Engineer I, Synthetic Chemistry to design and execute multi-step syntheses of novel drug-like molecules, including singleton analogs and small focused sets that cannot be made in plate format.

You will own route selection, execution, purification, and characterization end to end. Computational route planning, retrosynthesis, condition prediction, and automated or high-throughput experimentation resources will be standard working tools—not occasional aids. You will consume model output, judge when it is useful, correct it when it is not, and feed outcomes back into the planning and prediction workflows.

The ideal candidate is an accomplished bench chemist who is also fluent in computer-aided synthesis planning (CASP), reaction-prediction tools, and reaction data. You will be the resident synthetic-chemistry judgment for this part of the design–make–test loop and will mentor junior chemists using the same tools. This is not a software or ML research position; it is a chemistry role for someone who wants to make computational workflows genuinely useful in practice.

• Design, select, and execute practical multi-step routes to novel drug‑like singleton compounds and focused sets under real constraints on time, materials, building blocks, and available resources.
• Apply a broad synthetic‑organic chemistry toolkit and own purification and characterization through delivery of high‑quality, well‑characterized compounds on schedule.

• Use computer‑aided synthesis planning, retrosynthesis, and reaction‑condition tools routinely; critically evaluate proposed routes and predictions and explain when they are implausible, impractical, or outside reliable coverage.
• Use chemical structure and reaction representations and building‑block catalogs to constrain plans to realistic starting materials, and design or interpret HTE and other reaction‑optimization experiments.
• Feed practical outcomes and corrected synthetic judgment back into planning, prediction, and cheminformatics workflows.

• Record every campaign, including failures, in structured, machine-readable form covering conditions, stoichiometry, outcomes, analytical data, and negative results.
• Design chemistry for automation and parallel execution where useful, while recognizing when a route genuinely requires manual bench work.
• Collaborate with chemists, computational scientists, and software engineers to define useful tools, make go/no-go heuristics explicit, and mentor junior chemists.

• Ph.D. in synthetic organic chemistry, medicinal chemistry, or a closely related field, plus 3 years of relevant industry or postdoctoral experience; or an M.S. with 6 years, or a B.S. with 9 years, of relevant experience.
• Demonstrated ability to design and execute multi‑step syntheses, including routes of approximately five or more steps through characterized final compounds, and to deliver compounds on schedule.
• Independent route‑design…