Senior Scientist – Molecular Design & Synthesis

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Position Summary

We are seeking a highly motivated Senior Scientist, Molecular Design & Synthesis to drive the design, synthesis, and optimization of novel molecular architectures that enable next-generation sequencing technologies.

This role combines hands-on molecular synthesis with computational molecular design and cheminformatics. The successful candidate will contribute across the full Design-Make-Test-Learn (DMTL) cycle, applying computational and data-driven approaches to generate innovative molecular designs and leveraging experimental chemistry to synthesize, characterize, and validate those concepts.

The ideal candidate thrives at the intersection of chemistry and computation, translating molecular hypotheses into experimentally testable constructs while generating insights that guide future design strategies. Experience applying cheminformatics, molecular modeling, machine learning, or related computational approaches to accelerate molecular design and synthetic chemistry programs is strongly preferred.

Key ResponsibilitiesMolecular Design & Cheminformatics (40-50%)

• Design and optimize novel molecular constructs using structure-property-function relationships and mechanistic insights.
• Apply cheminformatics, molecular modeling, computational chemistry, and data-driven approaches to guide molecular design and prioritization.
• Build, curate, and analyze molecular datasets to identify trends, establish design principles, and generate testable hypotheses.
• Analyze experimental results and develop predictive models that correlate molecular features with performance.
• Evaluate molecular properties including conformation, solubility, charge distribution, hydrophobicity, linker behavior, and other factors that influence molecular function.
• Utilize computational tools such as RDKit, Python, molecular visualization software, and property prediction workflows to accelerate design cycles.
• Assess and implement emerging artificial intelligence and machine learning approaches to enhance molecular design and optimization.
• Assess synthetic feasibility and develop design strategies that balance molecular performance, manufacturability, scalability, and experimental throughput.

Molecular Synthesis & Characterization (40-50%)

• Design and execute synthetic routes for peptides, oligonucleotides, linkers, conjugates, and other novel molecular constructs.
• Perform and optimize syntheses using techniques that may include: Solid-phase peptide synthesis (SPPS) Oligonucleotide phosphoramidite synthesis Click chemistry Bioconjugation chemistry Synthetic organic chemistry methodologies
• Troubleshoot synthetic challenges and develop innovative solutions to improve yield, purity, scalability, and robustness.
• Characterize molecules using analytical techniques including LC-MS, analytical and preparative HPLC, spectroscopy, and other relevant methods.
• Maintain accurate experimental documentation and effectively communicate scientific findings through technical reports, presentations, and cross-functional discussions.

Project Leadership & Innovation (10-20%)

• Drive Design-Make-Test-Learn workflows across molecular development programs.
• Collaborate effectively with cross-functional teams spanning chemistry, biology, engineering, sequencing technology, bioinformatics, and data science.
• Generate innovative concepts and contribute to intellectual property development, including invention disclosures and patent applications.
• Provide technical leadership and mentorship to junior scientists and project team members.
• Present scientific findings, recommendations, and strategic insights to project teams and leadership.
• Identify technical risks and develop mitigation strategies within areas of responsibility and at critical cross-functional interfaces.
• Influence project direction through scientific expertise, critical thinking, and effective stakeholder engagement.

Listed responsibilities are intended to describe the general nature and level of work performed and are not intended to be an exhaustive list of all responsibilities associated with the position. Responsibilities may evolve based on business and project needs.

Success in the Role

The successful candidate will:

• Generate innovative molecular designs informed by computational and experimental insights.
• Efficiently develop, synthesize, and characterize novel molecular constructs that advance next-generation sequencing technologies.
• Establish predictive design principles that improve molecular performance and accelerate development cycles.
• Reduce experimental screening burden through rational, data-driven design approaches.
• Generate valuable intellectual property and contribute to technology differentiation.
• Serve as a key scientific bridge between computational design and experimental chemistry capabilities.
• Drive scientific innovation while enabling informed decision-making across multidisciplinary project teams.

Position Requirements

• Demonstrated expertise in molecular design, synthetic chemistry, and molecular characterization.
• Proven track record of independently driving complex scientific projects from concept through execution.
• Experience integrating computational and experimental approaches to address challenging scientific problems.
• Advanced understanding of scientific principles within a relevant discipline, with the ability to apply that knowledge creatively to novel problems.
• Demonstrated breadth of expertise across multiple scientific disciplines, technologies, or project areas.
• Ability to independently identify, prioritize, and execute high-impact work with minimal supervision.
• Ability to influence technical decisions and effectively engage stakeholders across functional boundaries.
• Strong written, verbal, and presentation skills, with the ability to communicate complex scientific concepts to diverse audiences.
• Experience mentoring scientists and contributing to a culture of scientific excellence is preferred.

All listed requirements are considered essential functions of this position; however, reasonable accommodations may be made to enable qualified individuals to perform the essential functions of the role.

Preferred Experience / Education / Skills

• PhD in Chemistry, Medicinal Chemistry, Chemical Biology, Computational Chemistry, Chemical Engineering, or a related scientific discipline.
• Experience in one or more of the following areas: Peptide synthesis Oligonucleotide chemistry Bioconjugation chemistry Molecular modeling Cheminformatics Computational chemistry Structure-property relationship analysis Machine learning for molecular design
• Experience with RDKit, Python, molecular modeling software, or related computational tools.
• Experience generating intellectual property and contributing to patent applications.
• Experience working within multidisciplinary research and development environments.
• Typically requires a minimum of 5 years of related experience with a Bachelor's degree, 3 years with a Master's degree, a PhD with relevant research experience, or equivalent industry experience.

We are a company deeply rooted in belonging, promoting an inclusive environment where employees feel valued and empowered to contribute to our mission. Built on a strong foundation, Illumina has always prioritized openness, collaboration, and seeking alternative perspectives to propel innovation in genomics. We are proud to confirm a zero-net gap in pay, regardless of gender, ethnicity, or race. We also have several Employee Resource Groups (ERG) that deliver career development experiences, increase cultural awareness, and offer opportunities to engage in social responsibility. We are proud to be an equal opportunity employer committed to providing employment opportunity regardless of sex, race, creed, color, gender, religion, marital status, domestic partner status, age, national origin or ancestry, physical or mental disability, medical condition, sexual orientation, pregnancy, military or veteran status, citizenship status, and genetic information. Illumina conducts background checks on applicants for whom a conditional offer of employment has been made. Qualified applicants with arrest or conviction records will be considered for employment in accordance with applicable local, state, and federal laws. Background check results may potentially result in the withdrawal of a conditional offer of employment. The background check process and any decisions made as a result shall be made in accordance with all applicable local, state, and federal laws. Illumina prohibits the use of generative artificial intelligence (AI) in the application and interview process. If you require accommodation to complete the application or interview process, please contact [email protected]. To learn more, visit: https://www.dol.gov/ofccp/regs/compliance/posters/pdf/eeopost.pdf. The position will be posted until a final candidate is selected or the requisition has a sufficient number of qualified applicants. This role is not eligible for visa sponsorship.