Evidence map›Paper›PMID 40918357›Full record

ArticleACS omega2025

Thermodynamics of Molecular Binding and Clustering in the Atmosphere Revealed through Conventional and ML-Enhanced Umbrella Sampling.

Jakub Kubečka, Yosef Knattrup, Georg Baadsgaard Trolle, Bernhard Reischl, August Smart Lykke-Møller, Jonas Elm, Ivo Neefjes

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In one paragraph

Article in ACS omega, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Jakub KubečkaAarhus University, Department of Chemistry, Langelandsgade 140, Aarhus DK 8000, Denmark.ORCID https://orcid.org/0000-0002-8002-0911
Yosef KnattrupAarhus University, Department of Chemistry, Langelandsgade 140, Aarhus DK 8000, Denmark.ORCID https://orcid.org/0000-0003-3549-7494
Georg Baadsgaard TrolleAarhus University, Department of Chemistry, Langelandsgade 140, Aarhus DK 8000, Denmark.ORCID https://orcid.org/0009-0007-4888-7041
Bernhard ReischlUniversity of Helsinki, Institute for Atmospheric and Earth System Research (INAR)/Physics P.O.Box 64, Helsinki FI 00014, Finland.ORCID https://orcid.org/0000-0001-7333-4923
August Smart Lykke-MøllerAarhus University, Department of Chemistry, Langelandsgade 140, Aarhus DK 8000, Denmark.
Jonas ElmAarhus University, Department of Chemistry, Langelandsgade 140, Aarhus DK 8000, Denmark.ORCID https://orcid.org/0000-0003-3736-4329
Ivo NeefjesAarhus University, Department of Chemistry, Langelandsgade 140, Aarhus DK 8000, Denmark.ORCID https://orcid.org/0000-0003-4549-0114

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Accurately modeling the binding free energies associated with molecular cluster formation is critical for understanding atmospheric new particle formation. Conventional quantum-chemistry methods, however, often struggle to describe thermodynamic contributions, particularly in systems exhibiting significant anharmonicity and configurational complexity. We employed umbrella sampling, an enhanced-sampling molecular dynamics technique, to compute Gibbs binding free energies for clusters formed from a diverse set of new particle formation precursors, including sulfuric acid, ammonia, dimethylamine, and water. By performing umbrella sampling along the evaporation coordinate, using forces computed at the semiempirical GFN1-xTB level of theory, we effectively capture entropic effects such as vibrational anharmonicities and transitions between different configurational minima, while avoiding errors from symmetry overcounting. In addition, we explored machine-learning-enhanced umbrella sampling simulations using neural network potentials trained on higher-level quantum chemistry data, demonstrating the feasibility of this approach for improving accuracy while maintaining computational efficiency. Our results show improved agreement with experimental values compared to conventional methods. We also present examples of gas-to-particle uptake processes, providing insights into cluster and aerosol-surface chemistry using first-principles approaches rather than commonly used molecular-mechanics force fields. This study demonstrates the importance of accounting for dynamics in predicting molecular binding thermodynamics in complex environments and highlights the potential of combining physics-based simulations with machine learning for reliable and scalable predictions.

Identifiers

PMID40918357
PMCPMC12409561

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.