Cargando…
Improved Configurational Sampling Protocol for Large Atmospheric Molecular Clusters
[Image: see text] The nucleation process leading to the formation of new atmospheric particles plays a crucial role in aerosol research. Quantum chemical (QC) calculations can be used to model the early stages of aerosol formation, where atmospheric vapor molecules interact and form stable molecular...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
|
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688134/ https://www.ncbi.nlm.nih.gov/pubmed/38046341 http://dx.doi.org/10.1021/acsomega.3c06794 |
_version_ | 1785152119968366592 |
---|---|
author | Wu, Haide Engsvang, Morten Knattrup, Yosef Kubečka, Jakub Elm, Jonas |
author_facet | Wu, Haide Engsvang, Morten Knattrup, Yosef Kubečka, Jakub Elm, Jonas |
author_sort | Wu, Haide |
collection | PubMed |
description | [Image: see text] The nucleation process leading to the formation of new atmospheric particles plays a crucial role in aerosol research. Quantum chemical (QC) calculations can be used to model the early stages of aerosol formation, where atmospheric vapor molecules interact and form stable molecular clusters. However, QC calculations heavily depend on the chosen computational method, and when dealing with large systems, striking a balance between accuracy and computational cost becomes essential. We benchmarked the binding energies and structures and found the B97-3c method to be a good compromise between the accuracy and computational cost for studying large cluster systems. Further, we carefully assessed configurational sampling procedures for targeting large atmospheric molecular clusters containing up to 30 molecules (approximately 2 nm in diameter) and proposed a funneling approach with highly improved accuracy. We find that several parallel ABCluster explorations lead to better guesses for the cluster global energy minimum structures than one long exploration. This methodology allows us to bridge computational studies of molecular clusters, which typically reach only around 1 nm, with experimental studies that often measure particles larger than 2 nm. By employing this workflow, we searched for low-energy configurations of large sulfuric acid–ammonia and sulfuric acid–dimethylamine clusters. We find that the binding free energies of clusters containing dimethylamine are unequivocally more stable than those of the ammonia-containing clusters. Our improved configurational sampling protocol can in the future be applied to study the growth and dynamics of large clusters of arbitrary compositions. |
format | Online Article Text |
id | pubmed-10688134 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-106881342023-12-01 Improved Configurational Sampling Protocol for Large Atmospheric Molecular Clusters Wu, Haide Engsvang, Morten Knattrup, Yosef Kubečka, Jakub Elm, Jonas ACS Omega [Image: see text] The nucleation process leading to the formation of new atmospheric particles plays a crucial role in aerosol research. Quantum chemical (QC) calculations can be used to model the early stages of aerosol formation, where atmospheric vapor molecules interact and form stable molecular clusters. However, QC calculations heavily depend on the chosen computational method, and when dealing with large systems, striking a balance between accuracy and computational cost becomes essential. We benchmarked the binding energies and structures and found the B97-3c method to be a good compromise between the accuracy and computational cost for studying large cluster systems. Further, we carefully assessed configurational sampling procedures for targeting large atmospheric molecular clusters containing up to 30 molecules (approximately 2 nm in diameter) and proposed a funneling approach with highly improved accuracy. We find that several parallel ABCluster explorations lead to better guesses for the cluster global energy minimum structures than one long exploration. This methodology allows us to bridge computational studies of molecular clusters, which typically reach only around 1 nm, with experimental studies that often measure particles larger than 2 nm. By employing this workflow, we searched for low-energy configurations of large sulfuric acid–ammonia and sulfuric acid–dimethylamine clusters. We find that the binding free energies of clusters containing dimethylamine are unequivocally more stable than those of the ammonia-containing clusters. Our improved configurational sampling protocol can in the future be applied to study the growth and dynamics of large clusters of arbitrary compositions. American Chemical Society 2023-11-13 /pmc/articles/PMC10688134/ /pubmed/38046341 http://dx.doi.org/10.1021/acsomega.3c06794 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Wu, Haide Engsvang, Morten Knattrup, Yosef Kubečka, Jakub Elm, Jonas Improved Configurational Sampling Protocol for Large Atmospheric Molecular Clusters |
title | Improved Configurational
Sampling Protocol for Large
Atmospheric Molecular Clusters |
title_full | Improved Configurational
Sampling Protocol for Large
Atmospheric Molecular Clusters |
title_fullStr | Improved Configurational
Sampling Protocol for Large
Atmospheric Molecular Clusters |
title_full_unstemmed | Improved Configurational
Sampling Protocol for Large
Atmospheric Molecular Clusters |
title_short | Improved Configurational
Sampling Protocol for Large
Atmospheric Molecular Clusters |
title_sort | improved configurational
sampling protocol for large
atmospheric molecular clusters |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688134/ https://www.ncbi.nlm.nih.gov/pubmed/38046341 http://dx.doi.org/10.1021/acsomega.3c06794 |
work_keys_str_mv | AT wuhaide improvedconfigurationalsamplingprotocolforlargeatmosphericmolecularclusters AT engsvangmorten improvedconfigurationalsamplingprotocolforlargeatmosphericmolecularclusters AT knattrupyosef improvedconfigurationalsamplingprotocolforlargeatmosphericmolecularclusters AT kubeckajakub improvedconfigurationalsamplingprotocolforlargeatmosphericmolecularclusters AT elmjonas improvedconfigurationalsamplingprotocolforlargeatmosphericmolecularclusters |