Selected Publications
PyAR has been used in a range of chemistry problems beyond pure algorithm development. This page highlights a few representative papers so a student or researcher can see what kinds of questions the workflows have already been used to study. The list is selective rather than exhaustive.
Aggregation And Clusters
PyAR’s aggregation and cluster-building workflows are useful whenever the problem is to grow a low-energy structure from smaller fragments.
[Nandi2017] Tabu-guided build-up for molecular aggregates and binary reactions.
[Khatun2019] Cluster optimization and global search for nanoclusters.
[Sherpa2026] Noncovalent-cluster application of the build-up workflow.
Reaction Discovery And Prebiotic Chemistry
PyAR’s AFIR-based reaction workflow is suitable for exploring products, reaction pathways, and chemically plausible intermediates.
[Nandi2018] Automated reaction search for prebiotic HCN tetramerization.
[Panda2024] Prebiotic reaction channels in an extraterrestrial atmosphere.
Catalyst Formation And Sequential Ligand Addition
The same reaction-search machinery can also follow stepwise ligand addition or catalyst assembly.
[Roy2022] Active catalyst formation from dinuclear palladium acetate by sequential ligand addition.
Exploration Of Chemical Space
PyAR can also be used as a general build-up engine for exploring clusters and other parts of chemical space.
[Giri2025] Chemical-space exploration of noncovalent molecular clusters.
Next Steps
If you want to use PyAR for a similar chemistry problem:
start with Quickstart to choose the right command
use Workflow Internals to see what each workflow writes to disk
use Usage for helper commands and analysis tools
References
Surajit Nandi, S. R. McAnanama-Brereton, M. P. Waller, and Anakuthil Anoop, A tabu-search based strategy for modeling molecular aggregates and binary reactions, Computational and Theoretical Chemistry 1111, 69-81 (2017). https://doi.org/10.1016/j.comptc.2017.03.040
Maya Khatun, Rajat Shubhro Majumdar, and Anakuthil Anoop, A Global Optimizer for Nanoclusters, Frontiers in Chemistry 7:644 (2019). https://doi.org/10.3389/fchem.2019.00644
Lazumla T. Sherpa, Maya Khatun, Sunanda Panda, and Anakuthil Anoop, Cooperative many-body interactions and spectroscopic signatures in (HCN)_{n} and (HNC)_{n} clusters up to n = 15, Physical Chemistry Chemical Physics 28, 2227-2238 (2026). https://doi.org/10.1039/D5CP03273C
Surajit Nandi, Debankur Bhattacharyya, and Anakuthil Anoop, Prebiotic Chemistry of HCN Tetramerization by Automated Reaction Search, Chemistry - A European Journal 24(19), 4885-4894 (2018). https://doi.org/10.1002/chem.201705492
Sunanda Panda and Anakuthil Anoop, Potential Prebiotic Pathways in Extraterrestrial Atmosphere: A Computational Exploration of HCN and NH_{3} Reactions, ACS Earth and Space Chemistry (2024). https://doi.org/10.1021/acsearthspacechem.3c00321
Saikat Roy and Anakuthil Anoop, Insights into the Active Catalyst Formation from Dinuclear Palladium Acetate in Pd-Catalyzed Coupling Reactions: A DFT Study, The Journal of Physical Chemistry A 126(46), 8562-8576 (2022). https://doi.org/10.1021/acs.jpca.2c03762
Sandip Giri and Anakuthil Anoop, Exploring the Chemical Space of Noncovalent Molecular Clusters Using Automated Cluster Building Algorithm and Neural Network Potential, Journal of Computational Chemistry 46(32), e70287 (2025). https://doi.org/10.1002/jcc.70287