Senior Computational Synthetic Chemist - AI-Driven Synthesis

Ginkgo BioWorks; Boston (MA); On-site; USD 115,000 - 165,000; Full time

Benefits offered by this job

Generous equity

Comprehensive benefits

401(k) with employer contribution

Job summary

Ginkgo Bioworks is seeking a Senior Engineer I in Computational Synthetic Chemistry to design and execute multi-step syntheses of novel drug-like molecules. You will own route selection, execution, purification, and characterization end to end, while integrating CASP tools and automated experimentation into practical workflows.

You will mentor junior chemists, evaluate predictions, and feed outputs back into planning to improve computational workflows and data quality.

Qualifications

• 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 judgment under real constraints on materials, time, building blocks, and execution resources, supported by a broad synthetic-organic reaction toolkit and strong purification and characterization skills.
• Routine hands-on use of computer-aided synthesis planning or retrosynthesis tools, with the judgment to recognize when a proposed route or prediction should not be trusted.
• Fluency with chemical structure and reaction data, including molecular and reaction representations, compound registration, stereochemistry, salts, tautomers, and building-block catalogs.
• Experience with reaction screening, HTE, design of experiments, or related optimization workflows, plus disciplined structured capture of conditions, outcomes, analytical results, and failures.

Responsibilities

• 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.

Skills

Computational chemistry

Go/No-Go judgement

Mentoring juniors

Tools

Python scripting

RDKit

Pandas

Jupyter

ELN/LIMS

Job description

Ginkgo Bioworks is seeking a Senior Engineer I in Computational Synthetic Chemistry to design and execute multi-step syntheses of novel drug-like molecules. You will own route selection, execution, purification, and characterization end to end, while integrating CASP tools and automated experimentation into practical workflows.

You will mentor junior chemists, evaluate predictions, and feed outputs back into planning to improve computational workflows and data quality.