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Kubečka J, Besel V, Neefjes I, Knattrup Y, Kurtén T, Vehkamäki H, Elm J. Computational Tools for Handling Molecular Clusters: Configurational Sampling, Storage, Analysis, and Machine Learning. ACS OMEGA 2023; 8:45115-45128. [PMID: 38046354 PMCID: PMC10688175 DOI: 10.1021/acsomega.3c07412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023]
Abstract
Computational modeling of atmospheric molecular clusters requires a comprehensive understanding of their complex configurational spaces, interaction patterns, stabilities against fragmentation, and even dynamic behaviors. To address these needs, we introduce the Jammy Key framework, a collection of automated scripts that facilitate and streamline molecular cluster modeling workflows. Jammy Key handles file manipulations between varieties of integrated third-party programs. The framework is divided into three main functionalities: (1) Jammy Key for configurational sampling (JKCS) to perform systematic configurational sampling of molecular clusters, (2) Jammy Key for quantum chemistry (JKQC) to analyze commonly used quantum chemistry output files and facilitate database construction, handling, and analysis, and (3) Jammy Key for machine learning (JKML) to manage machine learning methods in optimizing molecular cluster modeling. This automation and machine learning utilization significantly reduces manual labor, greatly speeds up the search for molecular cluster configurations, and thus increases the number of systems that can be studied. Following the example of the Atmospheric Cluster Database (ACDB) of Elm (ACS Omega, 4, 10965-10984, 2019), the molecular clusters modeled in our group using the Jammy Key framework have been stored in an improved online GitHub repository named ACDB 2.0. In this work, we present the Jammy Key package alongside its assorted applications, which underline its versatility. Using several illustrative examples, we discuss how to choose appropriate combinations of methodologies for treating particular cluster types, including reactive, multicomponent, charged, or radical clusters, as well as clusters containing flexible or multiconformer monomers or heavy atoms. Finally, we present a detailed example of using the tools for atmospheric acid-base clusters.
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Affiliation(s)
- Jakub Kubečka
- Aarhus
University, Department of Chemistry, Langelandsgade 140, Aarhus 8000, Denmark
| | - Vitus Besel
- University
of Helsinki, Institute for Atmospheric and
Earth System Research/Physics, Faculty of Science, P.O. Box 64, Helsinki 00140, Finland
| | - Ivo Neefjes
- University
of Helsinki, Institute for Atmospheric and
Earth System Research/Physics, Faculty of Science, P.O. Box 64, Helsinki 00140, Finland
| | - Yosef Knattrup
- Aarhus
University, Department of Chemistry, Langelandsgade 140, Aarhus 8000, Denmark
| | - Theo Kurtén
- University
of Helsinki, Institute for Atmospheric and
Earth System Research/Chemistry, Faculty of Science, P.O. Box 64, Helsinki 00140, Finland
| | - Hanna Vehkamäki
- University
of Helsinki, Institute for Atmospheric and
Earth System Research/Physics, Faculty of Science, P.O. Box 64, Helsinki 00140, Finland
| | - Jonas Elm
- Aarhus
University, Department of Chemistry, Langelandsgade 140, Aarhus 8000, Denmark
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