Thomas Mustard

The "Software Moat" is Dry: Why Scientists are the New Engineering Interns

The competitive advantage of scientific software is shifting. When AI can replicate proprietary workflows, the real moat becomes the data underneath them — and the scientists who know how to use it.

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The Evolution of a Catalytic Idea: From Academic Concept to Automated Discovery

Tracing the arc from a graduate-school question — can we automate catalyst design? — through a decade of building AutoRW, and into the current age of agentic scientific computing.

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Efficiency in Computational Chemistry III: The Coming Revolution in Process

When even the best individual tools aren't enough. The third part in the series examines why integrated, agentic systems are the next step in the evolution of scientific software.

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Efficiency in Computational Chemistry II: The Power of Automation and UX

How automation and thoughtful UX transformed computational chemistry from a specialist skill into something bench chemists could run — and what the tools that enabled this looked like from the inside.

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Go-to-Market for Deep Tech is Different: Here are 4 Principles for Success

The standard go-to-market playbook breaks when the product requires a PhD to evaluate. Four principles for navigating it, drawn from a decade of launching technical platforms for Fortune 50 clients.

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Efficiency in Computational Chemistry I

An early examination of where computational chemistry workflows were breaking down — not for lack of compute, but for lack of tools to manage, generate, and analyze data at scale. The gap identified here took a decade to close.

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True Autonomy Requires Orchestration, Not Just Prediction

An inside look at the Agentic AI Co-Researcher built at SandboxAQ — an orchestration layer where intelligent agents conduct research, plan multi-step workflows, execute simulations, and synthesize results to automate the full DMTA cycle at scale.

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The Holiday Gift That Wasn't (And Why Science is Still Hard)

An honest update on OINSMILES, an open-source project for the computational chemistry community. Not ready yet — not because the code is broken, but because the science is genuinely hard.

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One Hour, One GUI: What Google AI Studio Revealed About Scientific Tooling

Using Google AI Studio to convert a decade-old computational chemistry script into a working graphical interface in a single hour — and what that says about how scientists will build tools in the next decade.

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Selected Publications

  1. Dub, P. A.; Hughes, T.; Mustard, T. "A Software Framework for Physics- and AI-Driven Homogeneous Catalyst Design and Reactivity Optimization." ChemRxiv, 2025. DOI
  2. Allam, O.; Wander, B.; Kim, S.; et al.; Mustard, T. J.; et al. "AQCat25: Unlocking spin-aware, high-fidelity machine learning potentials for heterogeneous catalysis." arXiv, 2025. arXiv:2510.22938
  3. Mustard, T. J. L.; Afzal, M. A. F.; Sanders, J. M.; et al. "Multiscale modeling of polymers: Leveraging reaction kinetics for structural morphology and property prediction." Sampe neXus, 2021. DOI
  4. Sanders, J. M.; Misra, M.; Mustard, T. J.; et al. "Characterizing moisture uptake and plasticization effects of water on amorphous amylose starch models using molecular dynamics methods." Carbohydrate Polymers, 2021, 252, 117161. DOI
  5. Tsuchiya, Y.; Tsuji, K.; Inada, K.; et al.; Mustard, T. J.; et al. "Molecular design based on donor-weak donor scaffold for blue thermally-activated delayed fluorescence designed by combinatorial DFT calculations." Frontiers in Chemistry, 2020, 8, 403. DOI
  6. Matsuzawa, N. N.; Arai, H.; et al.; Mustard, T. J.; et al. "Massive theoretical screen of hole conducting organic materials in the heteroacene family by using a cloud-computing environment." J. Phys. Chem. A, 2020, 124, 1981–1992. DOI
  7. Mattson, E. C.; Cabrera, Y.; et al.; Mustard, T. J.; et al. "Chemical modification mechanisms in hybrid hafnium oxo-methacrylate nanocluster photoresists for extreme ultraviolet patterning." Chem. Mater., 2018, 30, 6192–6206. DOI
  8. Wills, L. A.; Qu, X.; Chang, I. Y.; Mustard, T. J.; et al. "Group additivity-Pourbaix diagrams advocate thermodynamically stable nanoscale clusters in aqueous environments." Nature Communications, 2017, 8, 1–7. DOI
  9. Mustard, T. J.; Wender, P. A.; Cheong, P. H. Y. "Catalytic efficiency is a function of how rhodium(I) (5+2) catalysts accommodate a conserved substrate transition state geometry." ACS Catalysis, 2015, 5, 1758–1763. DOI
  10. Yang, Y.; Mustard, T. J.; Cheong, P. H. Y.; Buchwald, S. L. "Palladium-Catalyzed Completely Linear-Selective Negishi Cross-Coupling of Allylzinc Halides with Aryl and Vinyl Electrophiles." Angew. Chem. Int. Ed., 2013, 52, 14098–14102. DOI
  11. Mustard, T. J.; Mack, D. J.; Njardarson, J. T.; Cheong, P. H. Y. "Mechanism and the origins of stereospecificity in copper-catalyzed ring expansion of vinyl oxiranes." J. Am. Chem. Soc., 2013, 135, 1471–1475. DOI
  12. Pattawong, O.; Mustard, T. J.; Johnston, R. C.; Cheong, P. H. Y. "Mechanism and Stereocontrol: Enantioselective Addition of Pyrrole to Ketenes Using Planar-Chiral Organocatalysts." Angew. Chem., 2013, 125, 1460–1463. DOI
Full list on Google Scholar