--- title: 'Computational Synthetic Chemist at Ginkgo Bioworks Inc.' canonical: 'https://feeny.ai/job/computational-synthetic-chemist-ginkgo-bioworks-inc-boston-ymnk9r1yjcph' type: 'job' last_seen: '2026-09-12' --- # Computational Synthetic Chemist at Ginkgo Bioworks Inc. - **Company:** Ginkgo Bioworks Inc. - **Location:** Boston, MA - **Posted:** 2026-08-24 - **Last confirmed live:** 2026-09-12 - **Apply:** https://job-boards.greenhouse.io/ginkgobioworks/jobs/5219763007 ## Job description 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. Senior Engineer I, Computational Synthetic Chemist Boston, Massachusetts ## About Ginkgo Datapoints Ginkgo Datapoints, 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, Datapoints 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. ## Role Overview 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. ## Key Responsibilities Multi-step synthesis and compound delivery - 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. Computationally enabled chemistry - 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. Data, automation, and collaboration - 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. ## Minimum 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. Working Style - You understand that computational models capture the current state of knowledge: they will never be perfect, but they can support learning and better decisions. You know the difference between useful guidance and an output that is not reliable enough to use. - You balance skepticism with practical progress. You make thoughtful go/no-go calls, state the limits of your judgment, and route unresolved questions to the right person or experiment rather than resolving them by assertion. - You are intellectually curious and impatient with the status quo, with a passion for establishing and advancing state-of-the-art chemistry workflows in practical production settings. ## Preferred Qualifications - Python scripting with tools such as RDKit, pandas, or Jupyter for manipulating compound sets, parsing analytical output, or prototyping analyses. - Experience running chemistry on robotic platforms, liquid handlers, flow systems, or other automated resources. - Industrial HTE or nanoscale reaction-screening experience. - Prior work in a CRO, fee-for-service, or similarly schedule-driven environment. - Experience with ELN/LIMS configuration or reaction-data model definition. - Experience scaling a validated route from milligram to multi-gram quantities. - Experience with inline or process monitoring such as ReactIR, benchtop NMR, or online LC-MS. - Experience mentoring or supervising junior chemists. - Publications or patents describing multi-step routes to biologically active compounds. Why Join Ginkgo Datapoints? - Help build the world’s most computationally enabled synthesis capability, combining expert chemistry with route planning, reaction prediction, automation, and learning. - Help connect route design, reaction prediction, synthesis, testing, and learning across Ginkgo’s automated platforms. - Develop workflows to capture, structure, and learn from the reaction data generated by autonomous laboratory systems. - Join a technically ambitious, cross-functional team building the computational foundations for AI-enabled drug discovery. - Receive competitive compensation, generous equity in a public company, and a robust benefits package. The base salary range for this role is $115,000–$165,000. Actual pay within this range will depend on a candidate's skills, expertise, and experience. We also offer company stock awards, a comprehensive benefits package including medical, dental & vision coverage, health spending accounts, voluntary benefits, leave of absence policies, 401(k) program with employer contribution, 8 paid holidays in addition to a full-week winter shutdown and unlimited Paid Time Off policy. Ginkgo has implemented a return to office policy effective October 1, 2025 with required in office days 5x per week. This policy applies to all employees who live within 50 miles of Ginkgo’s offices in Boston, MA, Emeryville, CA and West Sacramento, CA. It is the policy of Ginkgo Bioworks to provide equal employment opportunities to all employees, employment applicants, and EOE disability/vet. Privacy Notice I understand that I am applying for employment with Ginkgo Bioworks and am being asked to provide information in connection with my application. I further understand that Ginkgo gathers this information through a third-party service provider and that Ginkgo may also use other service providers to assist in the application process.  Ginkgo may share my information with such third-party service providers in connection with my application and for the start of employment.  Ginkgo will treat my information in accordance with Ginkgo's [Privacy Policy](https://www.ginkgobioworks.com/concentric-privacy-policy/).  By submitting this job application, I am acknowledging that I have reviewed and agree to Ginkgo's [Privacy Policy](https://www.ginkgobioworks.com/concentric-privacy-policy/) as well as the privacy policies of the third-party service providers used by Ginkgo's associated with the application process. ## About Ginkgo Bioworks Inc. ## Company Overview - **One-liner**: Ginkgo Bioworks builds and operates autonomous labs that replace manual benchwork with robotics, enabling scientists to program biology for applications across biopharma, agriculture, and industrial biotechnology. - **Entity Type**: Public (NYSE: DNA) - **Headquarters**: Boston, Massachusetts, United States - **Founded**: 2009 - **Founders**: Jason Kelly, Reshma Shetty, Barry Canton, Austin Che, Tom Knight ## Core Business - Primary industry: Biotechnology Research, Synthetic Biology, Autonomous Labs - Target customers: Biopharma, agriculture, and industrial biotech companies (B2B, Enterprise) - Mission: "Build the tools that make biology easier to engineer for everyone" — with a vision that "our children will program biology like we once programmed computers." ## Products & Services - **[Autonomous Lab Platform]**: A robotics-driven laboratory system where scientists can order experimental work to be run by robots, replacing manual benchwork. Available as Ginkgo’s in-house lab or as a "cloud lab" service. - **[Ginkgo Datapoints]**: A contract research service offering small molecule developability, high-throughput screening, and ADME (absorption, distribution, metabolism, excretion) services. - **[Ginkgo Solutions]**: Custom contract research and development services for customer-specific biotech projects. - **[Catalyst Agent]**: A tool that lets scientists "run your experiments on Ginkgo's autonomous lab in Boston, virtually." - **[Biosecurity Software]**: A software offering focused on biosecurity applications. ## Market Standing - **Valuation/Market Cap**: Publicly traded (NYSE: DNA); market cap fluctuates — as of mid-2025, the company had a market cap in the range of ~$1-2 billion (check current quote). IPO date: September 17, 2021. - **Total Funding**: $3.31 billion (cumulative, including IPO and post-IPO equity) - **Key Metric**: Annual Revenue — Not publicly available in search results; the company reports financials in SEC filings. Headcount: ~454 employees (-36% YoY, reflecting a significant restructuring). - **Notable Investors/Partners**: Flagship Pioneering, Takeda, Sanofi, Novartis, Bayer, and others. Key acquisitions include FGen (2022), Circularis Biotechnologies (2022), Altar (2022), Bitome (2022), and AgBiome’s GENESIS Platform (2024). - **Growth Signals**: Trusted by over 130 customers; operates in 10 countries; strong government partnerships (CEO Jason Kelly previously chaired the U.S. National Security Commission on Emerging Biotechnology); active job postings up 175% YoY (though from a low base). ## Competitive Advantages - **Autonomous Lab Leadership**: Ginkgo is pioneering the shift from manual benchwork to fully automated, robot-run labs — a significant moat in productivity and scalability. - **Founding Team**: Founders are pioneers in synthetic biology (e.g., Tom Knight is considered the "father of synthetic biology"; Jason Kelly chaired the U.S. National Security Commission on Emerging Biotechnology). - **Platform Approach**: The "cell programming platform" allows biology to be engineered more like software, enabling applications across diverse markets (food, fragrance, pharmaceuticals). - **Government & Biosecurity Ties**: Deep relationships with U.S. government agencies for biosecurity and national security applications. ## Strategic Focus - **Autonomous Lab Expansion**: Scaling the autonomous lab platform and making it available as a "cloud lab" to external customers. - **Commercialization**: Moving from R&D to commercial revenue through Datapoints and Solutions services. - **Cost Optimization**: The 36% headcount reduction suggests a focus on operational efficiency and path to profitability. - **Biosecurity**: Leveraging government partnerships for biosecurity software and services. ## Why Work Here - **Cutting-Edge Mission**: Work at the intersection of biology, robotics, and software — "program biology like we once programmed computers." - **Engineering Culture**: Heavy emphasis on software engineering for autonomous lab systems (robotics, scheduling, optimization, driver development) — roles for senior software engineers, automation engineers, and hardware engineers. - **Locations**: Primary hub in Boston, Massachusetts (headquarters); second office in Emeryville, California. Some remote roles (e.g., Director, Government Partnership Development). - **Culture**: Described as a place where scientists "focus on insight, creativity, and judgment rather than manual lab work." Internships available in software, automation, and commercial operations. - **Perks**: Not explicitly detailed in search results, but typical for a public biotech: equity, health benefits, and the chance to work on world-changing problems. - **Important Note**: The company has undergone a 36% headcount reduction in the past year — potential job seekers should be aware of restructuring and recent departures of senior leaders (e.g., Head of Commercial, Director of National Security partnerships). ## Sources 1. [ginkgo.bio](https://www.ginkgo.bio/) 2. [ginkgo.bio/about](https://ginkgo.bio/about) 3. [LinkedIn - Ginkgo Bioworks](https://www.linkedin.com/company/ginkgo-bioworks) 4. 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