Computational Chemist, Drug Discovery

About SandboxAQ

SandboxAQ is a high-growth company delivering AI solutions that address some of the world's greatest challenges. The company’s Large Quantitative Models (LQMs) power advances in life sciences, financial services, navigation, cybersecurity, and other sectors.

We are a global team that is tech-focused and includes experts in AI, chemistry, cybersecurity, physics, mathematics, medicine, engineering, and other specialties. The company emerged from Alphabet Inc. as an independent, growth capital-backed company in 2022, funded by leading investors and supported by a braintrust of industry leaders. 

At SandboxAQ, we’ve cultivated an environment that encourages creativity, collaboration, and impact. By investing deeply in our people, we’re building a thriving, global workforce poised to tackle the world's epic challenges. Join us to advance your career in pursuit of an inspiring mission, in a community of like-minded people who value entrepreneurialism, ownership, and transformative impact. 

About the Role

SandboxAQ’s AI Simulation team develops novel drugs and materials by integrating AI and physics-based computational solutions. Our AQBioSim group seeks a computational chemist who will not only apply cutting-edge methodologies but also critically assess and refine computational approaches. This individual will challenge assumptions, ask "why" when interpreting results, and ensure the reliability and accuracy of findings rather than blindly trusting outputs.

This role will drive innovation by combining quantum, AI, and physics-based methods—such as molecular dynamics and active learning free energy perturbation—to advance drug discovery. Working within a highly skilled and multidisciplinary team, including drug hunters with a strong track record in drug discovery, computational chemists, physicists, AI experts, and software engineers, you will play a key role in shaping the future of computational drug design.

What You’ll Do

• Apply computational solutions to address unmet drug discovery challenges, questioning assumptions and rigorously validating results.
• Work closely with the development team to enhance SandboxAQ’s unique technology and Large Quantitative Models (LQMs) for large-scale impact.
• Apply SandboxAQ’s computational platform to provide high-value drug discovery solutions while critically evaluating its methodologies and results.
• Translate insights from molecular dynamics, free energy perturbation, molecular docking, quantum, and ML methods into actionable, testable drug discovery hypotheses.
• Collaborate closely with ML experts and cross-functional teams to prototype and scale innovative drug design solutions.
• Develop and deploy computational methods and workflows to generate and evaluate hypotheses, guiding design decisions and influencing project direction.
• Challenge conventional thinking by critically assessing and interpreting computational outputs, ensuring robust scientific conclusions.
• Directly contribute to the discovery of innovative medicines by integrating computational chemistry techniques into multidisciplinary drug discovery teams.

About You

This role is ideal for someone who thrives in a questioning, analytical, and collaborative environment—someone who is not satisfied with merely generating results but is driven to understand the underlying mechanisms and refine methodologies for the most reliable and impactful outcomes.

• PhD in computational physics, computational chemistry, or a related discipline.
• 1-5 years of relevant experience, including hands-on experience with computational chemistry applied to drug discovery in biotech, pharma, or related industries.
• A deep commitment to critical thinking—comfortable questioning methodologies, challenging assumptions, and refining approaches to improve predictive accuracy.
• A collaborative mindset, working closely with colleagues to identify problems and communicate technical solutions clearly and effectively.
• A hands-on mentality, eager to dive into complex problems and drive projects to completion.
• Experience in structure-based drug design and familiarity with ligand-based drug design methods.
• Experience with GPU-accelerated MD codes like OpenMM.
• Proficiency in the Python data science stack (NumPy, Pandas, SciPy, etc.).
• Familiarity with ligand-protein free energy of binding prediction methods such as Free Energy Perturbation (FEP) or similar.
• Experience running computational chemistry/quantum simulations on high-performance computing (GPU) environments for corporate R&D, innovation labs, or academic research.
• A passion for solving scientific problems in chemistry and biology through computational and data-driven methods, with a commitment to rigorous validation and scientific integrity.

The US base salary range for this full-time position is expected to be $142k - $199k per year. Our salary ranges are determined by role and level. Within the range, individual pay is determined by factors including job-related skills, experience, and relevant education or training. This role may be eligible for annual discretionary bonuses and equity.

SandboxAQ welcomes all.

We are committed to creating an inclusive culture where we have zero tolerance for discrimination. We invest in our employees' personal and professional growth. Once you work with us, you can’t go back to normalcy because great breakthroughs come from great teams and we are the best in AI and quantum technology.   We offer competitive salaries, stock options depending on employment type, generous learning opportunities, medical/dental/vision, family planning/fertility, PTO (summer and winter breaks), financial wellness resources, 401(k) plans, and more.    Equal Employment Opportunity: All qualified applicants will receive consideration regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity, or Veteran status.   Accommodations: We provide reasonable accommodations for individuals with disabilities in job application procedures for open roles. If you need such an accommodation, please let a member of our Recruiting team know.