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From reproducibility to comparability in computational photochemistry: lessons from the PhotoChem explorer prototype
Open accessPublished version of a preprint
Abstract
Shared, structured representations can link excited-state dynamics studies into knowledge that is easier to understand, compare, and reuse. PhotoChem Explorer explores what it takes to support more cumulative knowledge building in computational photochemistry.
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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
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
The FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.18 · Cited by 18,423
Why Most Published Research Findings Are False
Ioannidis, J. P. A. (2005) · PLoS Medicine · doi:10.1371/journal.pmed.0020124 · Cited by 10,505
Weininger, D. (1988) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci00057a005 · Cited by 7,436
Molecular dynamics with electronic transitions
Tully, J. C. (1990) · The Journal of Chemical Physics · doi:10.1063/1.459170 · Cited by 3,985
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac956 · Cited by 3,443
A manifesto for reproducible science
Munafò, M. R., Nosek, B. A., Bishop, D. V. M., Button, K. S., Chambers, C. D., Percie du Sert, N., Simonsohn, U., Wagenmakers, E.-J., Ware, J. J., & Ioannidis, J. P. A. (2017) · Nature Human Behaviour · doi:10.1038/s41562-016-0021 · Cited by 3,397
Cambié, D., Bottecchia, C., Straathof, N. J. W., Hessel, V., & Noël, T. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00707 · Cited by 1,538
Protein Data Bank: the single global archive for 3D macromolecular structure data
wwPDB consortium, Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Costanzo, L. D., Christie, C., Duarte, J. M., Dutta, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky949 · Cited by 1,163
InChI, the IUPAC International Chemical Identifier
Heller, S. R., Mcnaught, A. D., Плетнев, И. В., Stein, S. E., & Tchekhovskoi, D. V. (2015) · Journal of Cheminformatics · doi:10.1186/s13321-015-0068-4 · Cited by 875
Ab Initio Multiple Spawning: Photochemistry from First Principles Quantum Molecular Dynamics
Ben-Nun, M., Quenneville, J., & Martínez, T. J. (2000) · The Journal of Physical Chemistry A · doi:10.1021/jp994174i · Cited by 834
3Dmol.js: molecular visualization with WebGL
Rego, N. B., & Koes, D. R. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu829 · Cited by 393
Quantum dynamics simulations using Gaussian wavepackets: the vMCG method
Richings, G. W., Polyak, I., Spinlove, K. E., Worth, G. A., Burghardt, I., & Lasorne, B. (2015) · International Reviews in Physical Chemistry · doi:10.1080/0144235x.2015.1051354 · Cited by 337
Wang, S., Witek, J., Landrum, G. A., & Riniker, S. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00025 · Cited by 253
Simultaneous observation of nuclear and electronic dynamics by ultrafast electron diffraction
Yang, J., Zhu, X., Nunes, J. P. F., Yu, J. K., Parrish, R. M., Wolf, T., Centurion, M., Gühr, M., Li, R., Liu, Y., et al. (2020) · Science · doi:10.1126/science.abb2235 · Cited by 174
Electronic Structure Methods for the Description of Nonadiabatic Effects and Conical Intersections
Matsika, S. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00074 · Cited by 161
Newton-X Platform: New Software Developments for Surface Hopping and Nuclear Ensembles
Barbatti, M., Bondanza, M., Crespo‐Otero, R., Démoulin, B., Dral, P. O., Granucci, G., Kossoski, F., Lischka, H., Mennucci, B., Mukherjee, S., et al. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00804 · Cited by 135
Scale-Up of Photochemical Reactions: Transitioning from Lab Scale to Industrial Production
Zondag, S. D. A., Mazzarella, D., & Noël, T. (2023) · Annual Review of Chemical and Biomolecular Engineering · doi:10.1146/annurev-chembioeng-101121-074313 · Cited by 129
Ginsparg, P. (2011) · Nature · doi:10.1038/476145a · Cited by 124
Libra: An open-Source “methodology discovery” library for quantum and classical dynamics simulations
Akimov, A. V. (2016) · Journal of Computational Chemistry · doi:10.1002/jcc.24367 · Cited by 110
A molecular perspective on Tully models for nonadiabatic dynamics
Ibele, L. M., & Curchod, B. F. E. (2020) · Physical Chemistry Chemical Physics · doi:10.1039/d0cp01353f · Cited by 101
Self-citationQuantics: A general purpose package for Quantum molecular dynamics simulations
Worth, G. A. (2019) · Computer Physics Communications · doi:10.1016/j.cpc.2019.107040 · Cited by 97
SmilesDrawer: Parsing and Drawing SMILES-Encoded Molecular Structures Using Client-Side JavaScript
Probst, D., & Reymond, J. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00425 · Cited by 81
The Quest to Simulate Excited-State Dynamics of Transition Metal Complexes
Zobel, J. P., & González, L. (2021) · JACS Au · doi:10.1021/jacsau.1c00252 · Cited by 69
The need to implement FAIR principles in biomolecular simulations
Amaro, R. E., Åqvist, J., Bahar, İ., et al. (2025) · Nature Methods · doi:10.1038/s41592-025-02635-0 · Cited by 67
Photochemistry in Medicinal Chemistry and Chemical Biology
Zhu, W., Empel, C., Pelliccia, S., Koenigs, R. M., Proschak, E., & Hernández‐Olmos, V. (2024) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.3c02109 · Cited by 55
Roadmap for Molecular Benchmarks in Nonadiabatic Dynamics
Cigrang, L. L. E., Curchod, B. F. E., Ingle, R. A., Kelly, A., Mannouch, J. R., Accomasso, D., Alijah, A., Barbatti, M., Chebbi, W., Došlić, N., et al. (2025) · The Journal of Physical Chemistry A · doi:10.1021/acs.jpca.5c02171 · Cited by 52
Self-citationBenchmarking non-adiabatic quantum dynamics using the molecular Tully models
Gómez, S., Spinlove, K. E., & Worth, G. A. (2023) · Physical Chemistry Chemical Physics · doi:10.1039/d3cp03964a · Cited by 43
Self-citationAvagliano, D., Bonfanti, M., Nenov, A., & Garavelli, M. (2022) · Journal of Computational Chemistry · doi:10.1002/jcc.26966 · Cited by 38
Self-citationMDRepo—an open data warehouse for community-contributed molecular dynamics simulations of proteins
Roy, A., Ward, E., Choi, I., Cosi, M., Edgin, T., Hughes, T., Islam, M. S., Khan, A. M., Kolekar, A., Rayl, M. L., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1109 · Cited by 27
Mukherjee, S., Mattos, R. S., Toldo, J. M., Lischka, H., & Barbatti, M. (2024) · The Journal of Chemical Physics · doi:10.1063/5.0203636 · Cited by 25
Green, A. E., Liu, Y., Allum, F., Graßl, M., Lenzen, P., Ashfold, M. N. R., Bhattacharyya, S., Cheng, X., Centurion, M., Crane, S. W., et al. (2025) · The Journal of Chemical Physics · doi:10.1063/5.0266559 · Cited by 19
Imaging the photochemical dynamics of cyclobutanone with MeV ultrafast electron diffraction
Wang, T., Jiang, H., Jin, C., Zou, X., Zhu, P., Jiang, T., He, F., & Xiang, D. (2025) · The Journal of Chemical Physics · doi:10.1063/5.0267186 · Cited by 18
Chemical control of excited-state reactivity of the anionic green fluorescent protein chromophore
List, N. H., Jones, C. M., & Martı́nez, T. J. (2024) · Communications Chemistry · doi:10.1038/s42004-024-01099-1 · Cited by 17
Self-citationGhosh, D., Spinlove, K. E., Greene, H. J. M., Lau, N. A., Gómez, S., Kao, M.-H., Whitaker, W., Clark, I. P., Malakar, P., Worth, G. A., et al. (2024) · Journal of the American Chemical Society · doi:10.1021/jacs.4c10965 · Cited by 17
Self-citationPhotodynamics of Gas‐Phase Pyruvic Acid Following Light Absorption in the Actinic Region
Hutton, L., & Curchod, B. F. E. (2022) · ChemPhotoChem · doi:10.1002/cptc.202200151 · Cited by 16
Self-citationHait, D., Lahana, D., Fajen, O. J., Paz, A. S. P., Unzueta, P. A., Rana, B., Lu, L., Wang, Y., Kjønstad, E. F., Koch, H., et al. (2024) · The Journal of Chemical Physics · doi:10.1063/5.0203800 · Cited by 16
Perspective on Theoretical and Experimental Advances in Atmospheric Photochemistry
Curchod, B. F. E., & Orr‐Ewing, A. J. (2024) · The Journal of Physical Chemistry A · doi:10.1021/acs.jpca.4c03481 · Cited by 16
Self-citationUnderstanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment
Choudhury, A., Santra, S., & Ghosh, D. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c00027 · Cited by 15
Photofragmentation of cyclobutanone at 200 nm: TDDFT vs CASSCF electron diffraction
Daría, A. M. S., Hernández-Rodríguez, J., Ibele, L. M., & Gómez, S. (2024) · The Journal of Chemical Physics · doi:10.1063/5.0197895 · Cited by 13
Self-citationPrediction through quantum dynamics simulations: Photo-excited cyclobutanone
Bennett, O., Freibert, A., Spinlove, K. E., & Worth, G. A. (2024) · The Journal of Chemical Physics · doi:10.1063/5.0203654 · Cited by 13
Imaging Valence Electron Rearrangement in a Chemical Reaction Using Hard X-Ray Scattering
Gabalski, I., Green, A. E., Lenzen, P., Allum, F., Bain, M., Bhattacharyya, S., Britton, M. A., Champenois, E. G., Cheng, X., Cryan, J., et al. (2025) · Physical Review Letters · doi:10.1103/53h3-vykl · Cited by 12
Self-citationSurface Hopping Nested Instances Training Set for Excited-state Learning
Curth, R., Röhrkasten, T. E., Müller, C., & Westermayr, J. (2025) · Scientific Data · doi:10.1038/s41597-025-05443-5 · Cited by 10
Best practices for nonadiabatic molecular dynamics simulations [Article v1.0]
Prlj, A., Taylor, J. T., Janoš, J., Lognon, E., Hollas, D., Slavíček, P., Agostini, F., & Curchod, B. F. E. (2026) · Living Journal of Computational Molecular Science · doi:10.33011/livecoms.7.1.4157 · Cited by 8
Self-citationChakraborty, P., Couto, R. C., & List, N. H. (2023) · The Journal of Physical Chemistry A · doi:10.1021/acs.jpca.3c02582 · Cited by 7
Self-citationAvagliano, D. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c01715 · Cited by 7
Self-citationAlsimaree, A. A., Samman, S. S., Almohyawi, A. M., Altass, H. M., Mir, J. M., & Ahmed, S. A. (2026) · RSC Advances · doi:10.1039/d5ra09833e · Cited by 7
AccFG: Accurate Functional Group Extraction and Molecular Structure Comparison
Liu, X., Swaminathan, S., Zubarev, D. Y., Ransom, B., Park, N. H., Schmidt, K., & Zhao, H. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c01317 · Cited by 6
Martyka, M., Jankowska, J., Lischka, H., & Dral, P. O. (2026) · Chemical Science · doi:10.1039/d5sc09557c · Cited by 4
Ibele, L. M., Adamo, C., & Avagliano, D. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c01200 · Cited by 3
Self-citationSHNITSEL - Surface Hopping Nested Instances Training Set for Excited-state Learning
Höllring, K., Röhrkasten, T. E., Hartinger, M., Dietschreit, J. C. B., Mai, S., & Müller, C. (2025) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.14910194 · Cited by 3
Electronic and Inertial Effects of Methylation on Excited-State Hydrogen Transfer
Chakraborty, P., Couto, R. C., & List, N. H. (2026) · The Journal of Physical Chemistry A · doi:10.1021/acs.jpca.5c07439 · Cited by 3
Self-citationAlbani, C., & Avagliano, D. (2026) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.6c00052 · Cited by 3
Self-citationshnitsel-tools : a toolkit for the full lifecycle of surface hopping trajectory data
Höllring, K., Röhrkasten, T. E., & Müller, C. (2026) · Digital Discovery · doi:10.1039/d5dd00299k · Cited by 2
Advancing Reproducibility and Open Data in Theoretical and Computational Chemistry
Amaro, R. E., Batista, V. S., Blumberger, J., Choong, Y. S., Corminbœuf, C., Cournia, Z., Cui, Q., Vivo, M. D., Evangelista, F. A., Gao, Y. Q., et al. (2026) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6c00733 · Cited by 2
Perspective on a challenge: predicting the photochemistry of cyclobutanonePreprint
Janoš, J., List, N. H., Orr‐Ewing, A. J., Suchan, J., Barbatti, M., Bennett, O., Brady, M., Carmona‐García, J., Crespo‐Otero, R., Eng, J., et al. (2026) · University of Birmingham Research Portal (University of Birmingham) · doi:10.48550/arxiv.2604.12749 · Cited by 1
Self-citationSolvent and field effects on photoinduced ring opening: dynamics of furan as a case study
Avagliano, D., Gómez, S., & Ibele, L. M. (2026) · Faraday Discussions · doi:10.1039/d6fd00099a · Cited by 1
Self-citation
Research works printed but not linked: 12
- UNESCO , UNESCO Recommendation on Open Science , 2021
- Chakraborty, 2024, Wiley Interdiscip. Rev.: Comput. Mol. Sci., 14, e1715
- American Institute of Physics Prediction Challenge , Cyclobutanone Photochemistry , 2024 , https://pubs.aip.org/collection/16531/Prediction-Challenge-Cyclobutanone-Photochemistry , accessed: 2026-04-22
- List, 2022, J. Chem. Sci., 13, 373
- Jones, 2021, J. Chem. Sci., 12, 11347
- Mai, 2018, Wiley Interdiscip. Rev.: Comput. Mol. Sci., 8, e1370
- MDDB Consortium MDPosit , 2026 , https://mdposit.mddbr.eu/ , accessed: 2026-05-08
- G.Landrum and R.contributors , RDKit: Open-Source Cheminformatics , 2025 , https://www.rdkit.org
- DOI Foundation DOI.org , 2026 , https://www.doi.org/
- Anysphere Cursor , 2026 , https://www.cursor.com
- Anthropic Claude , 2026 , https://www.anthropic.com/claude
- Gómez, 2024, Phys. Chem. Chem. Phys., 26, 1829, 10.1039/D3CP03964A · DOI
Metadata
- Authors
- List, N. H., Gómez, S., Ibele, L. M., Curchod, B. F. E., & Avagliano, D.
- Affiliations
- Science for Life Laboratory (SE)
- Universidad Autónoma de Madrid (ES)
- Centre National de la Recherche Scientifique (FR)
- University of Bristol (GB)
- Corresponding author
- List, Nanna H.
- Venue
- Faraday Discussions
- Publisher
- Royal Society of Chemistry (RSC)
- Published
- 2026
- ISSN
- 1359-6640 (ISSN-L)
- 1364-5498
- OpenAlex
- W7169779839
- Cited by
- 0
- References
- 58
- FWCI
- 0.00
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Faraday Discussions (publishedVersion, cc-by)
- ChemRxiv (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by)
- University of Birmingham Research Portal (University of Birmingham) (publishedVersion, cc-by)
- Explore Bristol Research (publishedVersion, cc-by)
- HAL AMU (submittedVersion)
- Bristol Research (University of Bristol) (submittedVersion, cc-by)
- Funders
- Vetenskapsrådet (2022-0287)
- Engineering and Physical Sciences Research Council (EP/V026690/1, EP/X026973/1, EP/Y01930X/1)
- Ministerio de Ciencia, Innovación y Universidades (PID2024-162002NB-I00, PID2024-155352NB-C21)
- Topics
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
- Keywords
- reproducibility, comparability, web platform, excited-state dynamics, gas-phase molecules
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