KinBot: Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces

<p> <img src="https://raw.githubusercontent.com/zadorlab/KinBot/master/graphics/kinbot_logo_V2.png" width="220" height="240" /> </p>

Description

This repository contains the KinBot code version 2.2.1, a tool for automatically searching for reactions on the potential energy surface.

If you are using this tool in scientific publications, please reference the following publications:

• Ruben Van de Vijver, Judit Zádor: KinBot: Automated stationary point search on potential energy surfaces, Comp. Phys. Comm., 2019, 248, 106947. https://doi.org/10.1016/j.cpc.2019.106947

@article{Vijver2020,
   author = {Van de Vijver, Ruben and Z\'ador, Judit},
   title = {KinBot: Automated stationary point search on potential energy surfaces},
   journal = {Comput. Phys. Commun.},
   volume = {248},
   pages = {106947},
   year = {2020},
   type = {Journal Article}
}

• Judit Zádor, Carles Martí, Ruben Van de Vijver, Sommer L. Johansen, Yoona Yang, Hope A. Michelsen, Habib N. Najm: Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces, J. Phys. Chem. A, 2023, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558

@article{Zador2022,
   author = {Z\'ador, Judit and Mart\'i, Carles and Van de Vijver, Ruben and Johansen, Sommer L. and Yang, Yoona and Michelsen, Hope A. and Najm, Habib N.},
   title = {Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces},
   journal = {J. Phys. Chem. A},
   volume = {127},
   pages = {565-588},
   year = {2023},
   type = {Journal Article}
}

We appreciate if you send us the DOI of your published paper that used KinBot, so we can feature it here below.

How to Install

KinBot can be installed both in three different ways, from the PyPI index (pip install), from the conda-forge repo (conda install) or by cloning this github repo and then install it locally.

PyPI

pip install kinbot

Note KinBot only works with Python >= 3.10.

conda-forge

conda install -c conda-forge kinbot

From Github

If you want to have the very last version of KinBot without waiting for a release or you want to modify KinBot acccording to your needs you can clone the project from github:

git clone git@github.com:zadorlab/KinBot.git

and then, from within the KinBot directory produced after cloning, type:

pip install -e .

Note If you want to modify KinBot yourself it's better to fork the project into your own repository and then clone it.

How to Run

To run a single-well exploration of KinBot, make an input file (e.g. input.json) and run:

kinbot input.json

To run a full PES search, make an input file (e.g. input.json) and run:

pes input.json

You can find additional command line arguments in the manual.

Documentation

See the wiki for keywords, and our tutorial for a more hands-on introduction to the code.

List of files in this project

See list.

Authors

• Judit Zádor (jzador@sandia.gov)
• Ruben Van de Vijver
• Amanda Dewyer
• Carles Martí
• Clément Soulié (csoulie@sandia.gov)

Papers using KinBot

1. Kjaersgaard, A., Zádor J., Zwier, T. S., Shiels, O.J., Sheps, L.: Measurement of the CH3SCH2O2 -> CH2SCH2OOH rate coefficient and mass spectrometric characterization of hydroperoxymethyl thioformate (HPMTF) at T = 400 – 550 K. J. Phys. Chem. A, 2025 accepted. https://doi.org/10.1021/acs.jpca.5c06279
2. Shiels, O. J., Kjaersgaard, A., Zádor, J., Sheps, L.: Low-temperature autooxidation of cyclopentanone and 3-pentanone: The critical role of competing radical chain-branching and chain inhibiting pathways. Phys. Chem. Chem. Phys., 2025 accepted. https://doi.org/10.1039/D5CP03403E
3. Osborn, D. L., Samanta, B. R., Soulié, C., Reisler, H., Zádor, J.: Chemistry of sugar formation in the gas phase: Following the activated aldehyde. J. Am. Chem. Soc., 2025 147, 32468–32479. https://doi.org/10.1021/jacs.5c05357
4. Hansen, N., Gaiser, N., Bierkandt, T., Oßwald, P., Köhler, M., Zádor, J., Hemberger, P.: Identification of dihydropentalenes as products of the molecular-weight growth reaction of cyclopentadienyl plus propargyl. J. Phys. Chem. A, 2025, 129, 1714-1725. https://doi.org/10.1021/acs.jpca.4c06549
5. Wang, Z.-M., Wang, D., Mansy, A. E., Tian, Z.-Y.: Pyrolysis and kinetic modeling investigation of 1-methoxy-2-propanol. Combust. Flame, 2025, 271, 113804. https://doi.org/10.1016/j.combustflame.2024.113804
6. Almeida, T. G., Martí, C., Kurtén, T., Zádor, J., Johansen, S. L.: Theoretical analysis of the OH-Initiated atmospheric oxidation reactions of imidazole. Phys. Chem. Chem. Phys., 2024, 26, 23570-23587. https://doi.org/10.1039/D4CP02103G
7. Yuan, E. C.-Y., Kumar, A., Guan, X., Hermes, E. D., Rosen, A. S., Zádor, J., Head-Gordon, T., Blau, S. M.: Analytical ab initio Hessian from a Deep Learning Potential for Transition State Optimization. Nat. Comm., 2024, 15, 8865. https://doi.org/10.1038/s41467-024-52481-5
8. Doner, A. C., Zádor, J., Rotavera, B.: Stereoisomer-dependent rate coefficients and reaction mechanisms of 2-ethyloxetanylperoxy radicals. Proc. Combust. Inst., 2024, 40, 105578. https://doi.org/10.1016/j.proci.2024.105578
9. Hansen, N. A, Price, T. D., Filardi, L. R., Gurses, S. M., Zhou, W., Hansen, N., Osborn, D. L. Zádor, J., Kronawitter, C. X.: The photoionization of methoxymethanol: Fingerprinting a reactive C2 oxygenate in a complex reactive mixture. J. Chem. Phys., 2024, 160, 124306. https://doi.org/10.1063/5.0197827
10. Martí, C., Devereux, C., Najm, H. N., Zádor, J.: Evaluation of rate coefficients in the gas-phase using a machine learned potential. J. Phys. Chem. A, 2024, 128, 1958–1971. https://doi.org/10.1021/acs.jpca.3c07872
11. Lang, J., Foley, C. D., Thawoos, S., Behzadfar, A., Liu, Y., Zádor, J., Suits, A. G.: Reaction dynamics of S(3P) with 1,3-butadiene and isoprene: Crossed beam scattering, low temperature flow experiments, and high-level electronic structure calculations. Farad. Discuss., 2024, 251, 550-572. https://doi.org/10.1039/D4FD00009A
12. Wang, D., Tian, Z.-Y., Zheng, Z.-H., Li, W., Wu, L.-N., Kuang, J.-J., Yang, J.-Z.: Experimental and modeling study of the n, n-dimethylformamide pyrolysis at atmospheric pressure. Combust. Flame, 2024, 260, 113240. https://doi.org/10.1016/j.combustflame.2023.113240
13. Wang, D. Dai, W.-K., Tian, Z.-Y., Liu, Y.-W., Wang, Z.-M., Wu, L.-N., Kuang, J.-J., Wang ,Q.-P., Xu, Q., Wang, Z.-D.: Theoretical and experimental study on the pyrolysis of N-methylpyrrolidone. J Anal Appl Pyrolysis, 2024, 183, 106751. https://doi.org/10.1016/j.jaap.2024.106751
14. Doner, A. C., Zádor, J., Rotavera, B.: Unimolecular reactions of 2,4-dimethyloxetanyl radicals. J. Phys. Chem A, 2023, 127, 2591–2600 https://doi.org/10.1021/acs.jpca.2c08290
15. Li, H., Lang, J., Foley, C. D., Zádor, J., Suits, A. G.: Sulfur (3P) reaction with conjugated dienes gives cyclization to thiophenes under single collision conditions. J. Phys. Chem. Letters, 2023, 14, 7611–7617. https://doi.org/10.1021/acs.jpclett.3c01953
16. Martí, C., Michelsen, H. A., Najm, H. N., Zádor, J.: Comprehensive kinetics on the C7H7 potential energy surface under combustion conditions. J. Phys. Chem. A, 2023, 127, 1941–1959. https://pubs.acs.org/doi/full/10.1021/acs.jpca.2c08035
17. Zádor, J, Martí, C., Van de Vijver, R., Johansen, S. L., Yang, Y., Michelsen, H. A., Najm, H. N.: Automated reaction kinetics of gas-phase organic species over multiwell potential energy surfaces. J. Phys. Chem. A, 2023, 127, 565–588. https://doi.org/10.1021/acs.jpca.2c06558
18. Lockwood, K. S., Ahmed, S. F., Huq, N. A., Stutzman, S. C., Foust, T. D., Labbe, N. J.: Advances in predictive chemistry enable a multi-scale rational design approach for biofuels with advantaged properties Sustainable Energy Fuels, 2022, 6, 5371-5383. https://doi.org/10.1039/D2SE00773H
19. Takahashi, L., Yoshida, S., Fujima, J., Oikawa, H., Takahashi, K.: Unveiling the reaction pathways of hydrocarbons via experiments, computations and data science. Phys. Chem. Chem. Phys., 2022, 24, 29841-29849. https://pubs.rsc.org/en/content/articlelanding/2022/CP/D2CP04499D
20. Doner, A. C., Zádor, J., Rotavera, B.: Stereoisomer-dependent unimolecular kinetics of 2,4-dimethyloxetane peroxy radicals. Faraday Discuss., 2022, 238, 295-319. https://doi.org/10.1039/D2FD00029F
21. Ramasesha, K., Savee, J. D., Zádor, J., Osborn, D. L.: A New Pathway for Intersystem Crossing: Unexpected Products in the O(3P) + Cyclopentene Reaction. J. Phys. Chem. A, 2021, 125 9785-9801. https://doi.org/10.1021/acs.jpca.1c05817
22. Rogers, C. O, Lockwood, K. S., Nguyen, Q. L. D., Labbe, N. J.: Diol isomer revealed as a source of methyl ketene from propionic acid unimolecular decomposition. Int. J. Chem. Kinet., 2021, 53, 1272–1284. https://doi.org/10.1002/kin.21532
23. Lockwood, K. S., Labbe, N. J.: Insights on keto-hydroperoxide formation from O2 addition to the beta-tetrahydrofuran radical. Proceedings of the Combustion Institute, 2021, 38, 1, 533. https://doi.org/10.1016/j.proci.2020.06.357
24. Sheps, L., Dewyer, A. L., Demireva, M., and Zádor, J.: Quantitative Detection of Products and Radical Intermediates in Low-Temperature Oxidation of Cyclopentane. J. Phys. Chem. A 2021, 125, 20, 4467. https://doi.org/10.1021/acs.jpca.1c02001
25. Zhang, J., Vermeire, F., Van de Vijver, R., Herbinet, O.; Battin-Leclerc, F., Reyniers, M.-F., Van Geem, K. M.: _Detailed experimental and kinetic modeling study of 3-carene pyrol