The DOI matches its Crossref record; 60 of the 60 references it cites were found in a registry or an index.
Computational Studies of Prebiotic Chemistry at the Age of Machine Learning: From Recent Breakthroughs to Future Revolutions
Open accessPublished version of a preprint
Abstract
The emergence of life from abiotic chemical systems remains a central and unresolved question in natural sciences. Understanding how simple molecules gave rise to the first biomolecules and self‐sustaining reaction networks requires integrating scarce experimental data with advanced computational methods. Machine learning (ML) is rapidly transforming research in prebiotic chemistry. In particular, ML‐based interatomic potentials enable the exploration of complex reaction mechanisms at near‐quantum accuracy and reduced computational cost. Beyond individual reactions, ML methods can also accelerate the study of chemical reaction networks by predicting transition states, reaction outcomes, and kinetic parameters. Here, we highlight recent methodological and conceptual advances, illustrating how ML complements traditional quantum chemical approaches. We further discuss emerging strategies for integrating data‐driven models with experimental and theoretical frameworks, expanding the scope and efficiency of research into the chemical origins of life.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Unified Approach for Molecular Dynamics and Density-Functional Theory
Car, R., & Parrinello, M. (1985) · Physical Review Letters · doi:10.1103/physrevlett.55.2471 · Cited by 10,754
Machine learning for molecular and materials science
Butler, K. T., Davies, D. W., Cartwright, H., Isayev, O., & Walsh, A. (2018) · Nature · doi:10.1038/s41586-018-0337-2 · Cited by 4,968
A Production of Amino Acids Under Possible Primitive Earth Conditions
Miller, S. L. (1953) · Science · doi:10.1126/science.117.3046.528 · Cited by 3,522
Recent advances and applications of machine learning in solid-state materials science
Schmidt, J., Marques, M. R. G., Botti, S., & Marques, M. A. L. (2019) · npj Computational Materials · doi:10.1038/s41524-019-0221-0 · Cited by 2,795
Unke, O. T., Chmiela, S., Sauceda, H. E., Gastegger, M., Poltavsky, I., Schütt, K. T., Tkatchenko, A., & Müller, K.-R. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.0c01111 · Cited by 1,647
Marx, D., & Hutter, J. (2009) · Cambridge University Press eBooks · doi:10.1017/cbo9780511609633 · Cited by 1,543
Chyba, C., & Sagan, C. (1992) · Nature · doi:10.1038/355125a0 · Cited by 1,321
Prebiotic Systems Chemistry: New Perspectives for the Origins of Life
Ruiz-Mirazo, K., Briones, C., & de la Escosura, A. (2014) · Chemical Reviews · doi:10.1021/cr2004844 · Cited by 930
Four Generations of High-Dimensional Neural Network Potentials
Behler, J. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.0c00868 · Cited by 873
Prediction of Organic Reaction Outcomes Using Machine Learning
Coley, C. W., Barzilay, R., Jaakkola, T., Green, W. H., & Jensen, K. F. (2017) · ACS Central Science · doi:10.1021/acscentsci.7b00064 · Cited by 773
Robertson, M. P., & Joyce, G. F. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003608 · Cited by 556
Organic compounds on comet 67P/Churyumov-Gerasimenko revealed by COSAC mass spectrometry
Goesmann, F., Rosenbauer, H., Bredehöft, J. H., Cabane, M., Ehrenfreund, P., Gautier, T., Giri, C., Krüger, H., Roy, L. L., MacDermott, A. J., et al. (2015) · Science · doi:10.1126/science.aab0689 · Cited by 499
MACE-OFF: Short-Range Transferable Machine Learning Force Fields for Organic Molecules
Kovács, D. P., Moore, J. H., Browning, N. J., Batatia, I., Horton, J. T., Pu, Y., Kapil, V., Witt, W. C., Magdău, I.-B., Cole, D. J., et al. (2025) · Journal of the American Chemical Society · doi:10.1021/jacs.4c07099 · Cited by 464
Machine Learning for Chemical Reactions
Meuwly, M. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00033 · Cited by 437
Discovering chemistry with an ab initio nanoreactor
Wang, L.-P., Titov, A., McGibbon, R., Liu, F., Pande, V. S., & Martínez, T. J. (2014) · Nature Chemistry · doi:10.1038/nchem.2099 · Cited by 422
Biological Phosphoryl-Transfer Reactions: Understanding Mechanism and Catalysis
Lassila, J. K., Zalatan, J. G., & Herschlag, D. (2011) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060409-092741 · Cited by 414
The Origin of Life—Out of the Blue
Sutherland, J. D. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201506585 · Cited by 401
The eightfold path to non-enzymatic RNA replication
Szostak, J. W. (2012) · Journal of Systems Chemistry · doi:10.1186/1759-2208-3-2 · Cited by 359
Ab initio molecular dynamics: basic concepts, current trends and novel applications
Tuckerman, M. E. (2002) · Journal of Physics: Condensed Matter · doi:10.1088/0953-8984/14/50/202 · Cited by 315
The search for the chemistry of life's origin
Eschenmoser, A. (2007) · Tetrahedron · doi:10.1016/j.tet.2007.10.012 · Cited by 292
A practical guide to machine learning interatomic potentials – Status and future
Jacobs, R. M., Morgan, D. D., Attarian, S., Meng, J., Shen, C., Wu, Z., Xie, C. Y., Yang, J. H., Artrith, N., Blaiszik, B. J., et al. (2025) · Current Opinion in Solid State and Materials Science · doi:10.1016/j.cossms.2025.101214 · Cited by 290
The Exploration of Chemical Reaction Networks
Unsleber, J. P., & Reiher, M. (2020) · Annual Review of Physical Chemistry · doi:10.1146/annurev-physchem-071119-040123 · Cited by 216
Data Generation for Machine Learning Interatomic Potentials and Beyond
Kulichenko, M., Nebgen, B. T., Lubbers, N., Smith, J. S., Barros, K. M., Allen, A. E. A., Habib, A., Shinkle, E., Fedik, N. S., Li, Y. W., et al. (2024) · Chemical Reviews · doi:10.1021/acs.chemrev.4c00572 · Cited by 216
Large language models for disease diagnosis: a scoping review
Zhou, S., Xu, Z., Zhang, M., Xu, C., Guo, Y., Zhan, Z., Fang, Y., Ding, S., Wang, J., Xu, K., et al. (2025) · npj Artificial Intelligence · doi:10.1038/s44387-025-00011-z · Cited by 192
Zhang, S., Makoś, M. Z., Jadrich, R. B., Kraka, E., Barros, K. M., Nebgen, B. T., Tretiak, S., Isayev, O., Lubbers, N., Messerly, R. A., et al. (2024) · Nature Chemistry · doi:10.1038/s41557-023-01427-3 · Cited by 154
Neural network potentials for chemistry: concepts, applications and prospects
Käser, S., Vazquez-Salazar, L. I., Meuwly, M., & Töpfer, K. (2022) · Digital Discovery · doi:10.1039/d2dd00102k · Cited by 134
Context-Driven Exploration of Complex Chemical Reaction Networks
Simm, G. N. C., & Reiher, M. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00945 · Cited by 133
Gomez, A., Thompson, W. H., & Laage, D. (2024) · Nature Chemistry · doi:10.1038/s41557-024-01593-y · Cited by 126
The place of metabolism in the origin of life
Anet, F. A. L. (2004) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2004.10.005 · Cited by 114
Duan, C., Du, Y., Jia, H., & Kulik, H. J. (2023) · Nature Computational Science · doi:10.1038/s43588-023-00563-7 · Cited by 97
Chasing the tail: The emergence of autocatalytic networks
Hordijk, W., & Steel, M. (2016) · Biosystems · doi:10.1016/j.biosystems.2016.12.002 · Cited by 90
Prebiotic photoredox synthesis from carbon dioxide and sulfite
Liu, Z., Wu, L.-F., Kufner, C. L., Sasselov, D. D., Fischer, W. W., & Sutherland, J. D. (2021) · Nature Chemistry · doi:10.1038/s41557-021-00789-w · Cited by 70
Progress towards machine learning reaction rate constants
Komp, E., Janulaitis, N., & Valleau, S. (2021) · Physical Chemistry Chemical Physics · doi:10.1039/d1cp04422b · Cited by 60
Approximating solutions of the Chemical Master equation using neural networks
Sukys, A., Öcal, K., & Grima, R. (2022) · iScience · doi:10.1016/j.isci.2022.105010 · Cited by 58
Electron flow matching for generative reaction mechanism prediction
Joung, J. F., Fong, M. H., Casetti, N., Liles, J. P., Dassanayake, N. S., & Coley, C. W. (2025) · Nature · doi:10.1038/s41586-025-09426-9 · Cited by 58
Optimal transport for generating transition states in chemical reactions
Duan, C., Liu, G.-H., Du, Y., Chen, T., Zhao, Q., Jia, H., Gomes, C. P., Theodorou, E. A., & Kulik, H. J. (2025) · Nature Machine Intelligence · doi:10.1038/s42256-025-01010-0 · Cited by 57
Heat flows enrich prebiotic building blocks and enhance their reactivity
Matreux, T., Aikkila, P., Scheu, B., Braun, D., & Mast, C. B. (2024) · Nature · doi:10.1038/s41586-024-07193-7 · Cited by 52
Prebiotic chemistry and origins of life research with atomistic computer simulations
Pérez-Villa, A., Pietrucci, F., & Saitta, A. M. (2018) · Physics of Life Reviews · doi:10.1016/j.plrev.2018.09.004 · Cited by 47
Wilary, D. M., & Cole, J. M. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c00422 · Cited by 45
David, R., de la Puente, M., Gomez, A., Anton, O., Stirnemann, G., & Laage, D. (2024) · Digital Discovery · doi:10.1039/d4dd00209a · Cited by 42
Self-citationAlgorithmic Explorations of Unimolecular and Bimolecular Reaction Spaces**
Zhao, Q., & Savoie, B. M. (2022) · Angewandte Chemie International Edition · doi:10.1002/anie.202210693 · Cited by 38
Benayad, Z., David, R., & Stirnemann, G. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2322040121 · Cited by 35
Self-citationChen, H., Giese, T. J., Huang, M. S., Wong, K. Y., Harris, M. E., & York, D. M. (2014) · Chemistry - A European Journal · doi:10.1002/chem.201403862 · Cited by 33
Neural-network solutions to stochastic reaction networks
Tang, Y., Weng, J., & Zhang, P. (2023) · Nature Machine Intelligence · doi:10.1038/s42256-023-00632-6 · Cited by 33
Machine learning for nonadiabatic molecular dynamics: best practices and recent progress
Müller, C., Sršeň, Š., Bachmair, B., Crespo‐Otero, R., Li, J., Mausenberger, S., Pinheiro, M., Worth, G. A., Lopez, S. A., & Westermayr, J. (2025) · Chemical Science · doi:10.1039/d5sc05579b · Cited by 32
David, R., Tuñón, I., & Laage, D. (2024) · Journal of the American Chemical Society · doi:10.1021/jacs.4c03445 · Cited by 26
ANI-1xBB: An ANI-Based Reactive Potential for Small Organic Molecules
Zhang, S., Zubatyuk, R. I., Yang, Y., Roitberg, A. E., & Isayev, O. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c00347 · Cited by 25
Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives
Sharma, S., Arya, A., Cruz-Simbrón, R., & Cleaves, H. J. (2021) · Life · doi:10.3390/life11111140 · Cited by 24
Zhao, Q., Garimella, S. S., & Savoie, B. M. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.2c11857 · Cited by 23
Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism
Harris, M. E., Piccirilli, J. A., & York, D. M. (2015) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2015.04.022 · Cited by 22
Huang, M., & York, D. M. (2014) · Physical Chemistry Chemical Physics · doi:10.1039/c4cp01050g · Cited by 21
Chemical Reaction Networks from Scratch with Reaction Prediction and Kinetics-Guided Exploration
Woulfe, M., & Savoie, B. M. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c01401 · Cited by 19
Exploring Chemical Space Using Ab Initio Hyperreactor Dynamics
Stan-Bernhardt, A., Glinkina, L., Hulm, A., & Ochsenfeld, C. (2024) · ACS Central Science · doi:10.1021/acscentsci.3c01403 · Cited by 18
Vitartas, V., Zhang, H., Jurásková, V., Johnston-Wood, T., & Duarte, F. (2025) · Digital Discovery · doi:10.1039/d5dd00261c · Cited by 17
Achar, S. K., Shukla, P. B., Mhatre, C. V., Bernasconi, L., Vinger, C. Y., & Johnson, J. K. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c00920 · Cited by 11
A New Route to the Prebiotic Synthesis of Glycine via Ab Initio-Based Machine Learning Calculations
Huet, L., Devergne, T., Magrino, T., & Saitta, A. M. (2024) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.4c01954 · Cited by 10
A stepwise emergence of evolution in the RNA world
Nghe, P. (2025) · FEBS Letters · doi:10.1002/1873-3468.70065 · Cited by 9
Lifelong Machine Learning Potentials for Chemical Reaction Network Explorations
Eckhoff, M., & Reiher, M. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c01127 · Cited by 6
Modeling prebiotic chemistries with quantum accuracy at classical costs
Tiwary, P. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2408742121 · Cited by 4
Research works printed but not linked: 4
- B. M.Wood M.Dzamba X.Fu et al. “UMA: A Family of Universal Models for Atoms ”arXiv preprint(2025) https://doi.org/10.48550/arXiv.2506.23971. · DOI
- 10.26434/chemrxiv‐2025‐hpdmg · DOI
- 10.1088/2632-2153/abc81d · DOI · Paper page
- 10.1038/s41586-024-07193-7 · DOI
Metadata
- Authors
- Anton, O., & Stirnemann, G.
- Affiliations
- Université Paris Sciences et Lettres (FR)
- Corresponding author
- Stirnemann, Guillaume
- Venue
- ChemSystemsChem
- Publisher
- Wiley
- Published
- 2026-01
- Volume
- 8
- Issue
- 1
- ISSN
- 2570-4206 (ISSN-L)
- OpenAlex
- W7124186661
- Cited by
- 4
- References
- 60
- Citations by year
- 2026: 3
- FWCI
- 9.24
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- onlinelibrary.wiley.com/termsAndConditions#vor (vor, 13 d)
- doi.wiley.com/10.1002/tdm_license_1.1 (tdm)
- Locations
- ChemSystemsChem (publishedVersion)
- ChemRxiv (acceptedVersion, cc-by-nc)
- Funders
- H2020 European Research Council (757111)
- Topics
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Physical Sciences › Materials Science › Materials Chemistry › Machine Learning in Materials Science
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
- Keywords
- prebiotic chemistry, origin of life, machine learning interatomic potentials, reaction mechanism, reaction kinetics, chemical reaction networks
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.