The Kitchin Research Group

Suppose you want to explore metal oxides as potential water oxidation electrocatalysts. There are many steps to do this. You can use databases of materials to get compositions and structures, but for each one you have to determine the ground state structure, including magnetic states, for each bulk structure, and filter out bulk materials that are not stable under water oxidation conditions. Then, using the remaining structures you have to construct slabs and determine which surfaces are likely to be stable, and most relevant. After that you have to compute adsorption energies on those surfaces to see which surfaces have the most relevant reactivity (while also being stable). This results in hundreds to thousands of calculations that depend on each other in important ways. It is very useful to use software workflow tools to facilitate and manage this process. In this paper we develop a workflow like this for exploring metal oxides for water oxidation. The software is open source and available at https://github.com/ulissigroup/wherewulff.

The paper is free to read for 6 months at https://pubs.acs.org/doi/10.1021/acs.jcim.3c00142.

@article{sanspeur-2023,
  author = {Rohan Yuri Sanspeur and Javier Heras-Domingo and John R. Kitchin and Zachary Ulissi},
  title = {wherewulff: a Semiautonomous Workflow for Systematic Catalyst Surface Reactivity Under Reaction Conditions},
  journal = {Journal of Chemical Information and Modeling},
  volume = {nil},
  number = {nil},
  pages = {nil},
  year = {2023},
  doi = {10.1021/acs.jcim.3c00142},
  url = {http://dx.doi.org/10.1021/acs.jcim.3c00142},
  DATE_ADDED = {Sun Apr 16 09:17:23 2023},
}

Copyright (C) 2023 by John Kitchin. See the License for information about copying.

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Org-mode version = 9.5.5

Finding new ways to make hydrogen with renewable energy and renewable feedstocks using earth abundant materials remains a challenge in catalysis today. Metal nanoparticles are common heterogeneous catalysts for hydrogen production, and their properties can often be improved by using multiple metals at a time. In this work we show a high-throughput experimental approach to discovering a ternary alloy catalyst containing earth abundant metals that is more active at producing hydrogen than any of the pure metals it is made of. It a surprising discovery because these metals are not typically miscible, and they do not form a well characterized material, but rather a distribution of particle sizes and compositions.

@article{bhat-2023-high-throug,
  author = {Maya Bhat and Zoe C Simon and Savannah Talledo and Riti Sen and Jacob H. Smith and Stefan Bernhard and Jill E Millstone and John R Kitchin},
  title = {High Throughput Discovery of Ternary Cu-Fe-Ru Alloy Catalysts for Photo-Driven Hydrogen Production},
  journal = {Reaction Chemistry \& Engineering},
  volume = {nil},
  number = {nil},
  pages = {nil},
  year = {2023},
  doi = {10.1039/d3re00059a},
  url = {http://dx.doi.org/10.1039/D3RE00059A},
  DATE_ADDED = {Sat Apr 15 07:55:55 2023},
}

Copyright (C) 2023 by John Kitchin. See the License for information about copying.

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Org-mode version = 9.5.5

2022 was an interesting one. I still did all of my teaching remotely, but spent more time going in to the office for meetings, and have gotten back to professional travel for meetings.

2. Publications

Our work this past year was divided in a few efforts. We had some work in method development, e.g. in uncertainty quantification, automatic differentiation, and vector search.

1. Yang, Y., Achar, S. K., & Kitchin, J. R. (2022). Evaluation of the degree of rate control via automatic differentiation. AIChE Journal, 68(6). http://dx.doi.org/10.1002/aic.17653
2. Yang, Y., Liu, M., & Kitchin, J. R. (2022). Neural network embeddings based similarity search method for atomistic systems. Digital Discovery. http://dx.doi.org/10.1039/d2dd00055e
3. Zhan, N., & Kitchin, J. R. (2022). Model-specific to model-general uncertainty for physical properties. Industrial & Engineering Chemistry Research, 1–04706. http://dx.doi.org/10.1021/acs.iecr.1c04706

This collaborative work on large catalyst models is was especially exciting. Stay tuned for many advances in this area in 2023.

1. Kolluru, A., Shuaibi, M., Palizhati, A., Shoghi, N., Das, A., Wood, B., Zitnick, C. L., … (2022). Open challenges in developing generalizable large-scale machine-learning models for catalyst discovery. ACS Catalysis, 12(14), 8572–8581. http://dx.doi.org/10.1021/acscatal.2c02291

We also wrote some collaborative papers on our work in high-throughput discovery of hydrogen evolution catalysts and segregation.

1. Broderick, K., Lopato, E., Wander, B., Bernhard, S., Kitchin, J., & Ulissi, Z. (2022). Identifying limitations in screening high-throughput photocatalytic bimetallic nanoparticles with machine-learned hydrogen adsorptions. Applied Catalysis B: Environmental, 121959. http://dx.doi.org/10.1016/j.apcatb.2022.121959
2. Bhat, M., Lopato, E., Simon, Z. C., Millstone, J. E., Bernhard, S., & Kitchin, J. R. (2022). Accelerated optimization of pure metal and ligand compositions for light-driven hydrogen production. Reaction Chemistry & Engineering. http://dx.doi.org/10.1039/d1re00441g
3. Yilin Yang, Zhitao Guo, Andrew Gellman and John Kitchin, Simulating segregation in a ternary Cu-Pd-Au alloy with density functional theory, machine learning and Monte Carlo simulations, J. Phys. Chem. C, 126, 4, 1800-1808. (2022). https://pubs.acs.org/doi/abs/10.1021/acs.jpcc.1c09647

It was another big year in citations for us (https://scholar.google.com/citations?user=jD_4h7sAAAAJ)!

Copyright (C) 2023 by John Kitchin. See the License for information about copying.

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Hydrogen adsorption energies have long been used in screening to identify promising hydrogen evolution catalysts. In this work we combine a high-throughput experimental study of 5300 different bimetallic catalysts with a high-throughput computational screen of 16M adsorption energies to see how well adsorption energies work for this purpose. We developed a workflow to combine these data sets that accounts for surface stability and adsorption site distributions on alloy surfaces. We find that thermodynamically favorable adsorption energies are necessary to observe high activity, but they are not sufficient, and do not always lead to high activity.

@article{broderick-2022-ident-limit,
  author = {Kirby Broderick and Eric Lopato and Brook Wander and Stefan Bernhard and John Kitchin and Zachary Ulissi},
  title = {Identifying Limitations in Screening High-Throughput Photocatalytic Bimetallic Nanoparticles With Machine-Learned Hydrogen Adsorptions},
  journal = {Applied Catalysis B: Environmental},
  volume = {nil},
  number = {nil},
  pages = {121959},
  year = {2022},
  doi = {10.1016/j.apcatb.2022.121959},
  url = {http://dx.doi.org/10.1016/j.apcatb.2022.121959},
  DATE_ADDED = {Thu Sep 22 07:46:56 2022},
}

Copyright (C) 2022 by John Kitchin. See the License for information about copying.

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Org-mode version = 9.5.1

Searching for atomic structures in databases is like finding a needle in the haystack. It is difficult to construct a query that finds what you want, without finding nothing, or everything! It is difficult to use atomic coordinates because they are sensitive to translations, rotations and permutations. There are many ways to construct equivalent unit cells that also make it difficult to uniquely query materials.

In this paper we show how to construct queries for atomic structures that allow you to quickly find similar atomic structures. We achieve this by using invariant fingerprint vectors from machine learning models coupled with approximate nearest neighbor vector search algorithms. We apply it to molecules, bulk materials and adsorbates on surfaces. We show how the geometric similarity in found atomic systems leads to better data sets for building new machine learning models, and that the found systems tend to show geometric and electronic structure similarity.

You can read more about this work here (it is Open Access): Yilin Yang, Mingie Liu, John Kitchin, Digital Discovery, 2022, https://doi.org/10.1039/D2DD00055E

@article{yang-2022-neural-networ,
  author =       {Yilin Yang and Mingjie Liu and John R. Kitchin},
  title =        {Neural Network Embeddings Based Similarity Search Method for
                  Atomistic Systems},
  journal =      {Digital Discovery},
  volume =       {},
  number =       {},
  pages =        {},
  year =         2022,
  doi =          {10.1039/d2dd00055e},
  url =          {https://doi.org/10.1039/D2DD00055E},
  DATE_ADDED =   {Mon Sep 12 17:21:30 2022},
}

Copyright (C) 2022 by John Kitchin. See the License for information about copying.

org-mode source

Org-mode version = 9.5.1