1
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Engsvang M, Wu H, Elm J. Iodine Clusters in the Atmosphere I: Computational Benchmark and Dimer Formation of Oxyacids and Oxides. ACS OMEGA 2024; 9:31521-31532. [PMID: 39072118 PMCID: PMC11270685 DOI: 10.1021/acsomega.4c01235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/30/2024]
Abstract
The contribution of iodine-containing compounds to atmospheric new particle formation is still not fully understood, but iodic acid and iodous acid are thought to be significant contributors. While several quantum chemical studies have been carried out on clusters containing iodine, there is no comprehensive benchmark study quantifying the accuracy of the applied methods. Here, we present the first study in a series that investigate the role of iodine species in atmospheric cluster formation. In this work, we have studied the iodic acid, iodous acid, iodine tetroxide, and iodine pentoxide monomers and their dimers formed with common atmospheric precursors. We have tested the accuracy of commonly applied methods for calculating the geometry of the monomers, thermal corrections of monomers and dimers, the contribution of spin-orbit coupling to monomers and dimers, and finally, the accuracy of the electronic energy correction calculated at different levels of theory. We find that optimizing the structures either at the ωB97X-D3BJ/aug-cc-pVTZ-PP or the M06-2X/aug-cc-pVTZ-PP level achieves the best thermal contribution to the binding free energy. The electronic energy correction can then be calculated at the ZORA-DLPNO-CCSD(T0) level with the SARC-ZORA-TZVPP basis for iodine and ma-ZORA-def2-TZVPP for non-iodine atoms. We applied this methodology to calculate the binding free energies of iodine-containing dimer clusters, where we confirm the qualitative trends observed in previous studies. However, we identify that previous studies overestimate the stability of the clusters by several kcal/mol due to the neglect of relativistic effects. This means that their contributions to the currently studied nucleation pathways of new particle formation are likely overestimated.
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Affiliation(s)
- Morten Engsvang
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Haide Wu
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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2
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Knattrup Y, Kubečka J, Wu H, Jensen F, Elm J. Reparameterization of GFN1-xTB for atmospheric molecular clusters: applications to multi-acid-multi-base systems. RSC Adv 2024; 14:20048-20055. [PMID: 38911834 PMCID: PMC11191700 DOI: 10.1039/d4ra03021d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/16/2024] [Indexed: 06/25/2024] Open
Abstract
Atmospheric molecular clusters, the onset of secondary aerosol formation, are a major part of the current uncertainty in modern climate models. Quantum chemical (QC) methods are usually employed in a funneling approach to identify the lowest free energy cluster structures. However, the funneling approach highly depends on the accuracy of low-cost methods to ensure that important low-lying minima are not missed. Here we present a reparameterized GFN1-xTB model based on the clusteromics I-V datasets for studying atmospheric molecular clusters (AMC), denoted AMC-xTB. The AMC-xTB model reduces the mean of electronic binding energy errors from 7-11.8 kcal mol-1 to roughly 0 kcal mol-1 and the root mean square deviation from 7.6-12.3 kcal mol-1 to 0.81-1.45 kcal mol-1. In addition, the minimum structures obtained with AMC-xTB are closer to the ωB97X-D/6-31++G(d,p) level of theory compared to GFN1-xTB. We employ the new parameterization in two new configurational sampling workflows that include an additional meta-dynamics sampling step using CREST with the AMC-xTB model. The first workflow, denoted the "independent workflow", is a commonly used funneling approach with an additional CREST step, and the second, the "improvement workflow", is where the best configuration currently known in the literature is improved with a CREST + AMC-xTB step. Testing the new workflow we find configurations lower in free energy for all the literature clusters with the largest improvement being up to 21 kcal mol-1. Lastly, by employing the improvement workflow we massively screened 288 new multi-acid-multi-base clusters containing up to 8 different species. For these new multi-acid-multi-base cluster systems we observe that the improvement workflow finds configurations lower in free energy for 245 out of 288 (85.1%) cluster structures. Most of the improvements are within 2 kcal mol-1, but we see improvements up to 8.3 kcal mol-1. Hence, we can recommend this new workflow based on the AMC-xTB model for future studies on atmospheric molecular clusters.
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Affiliation(s)
- Yosef Knattrup
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
| | - Jakub Kubečka
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
| | - Haide Wu
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
| | - Frank Jensen
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
| | - Jonas Elm
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
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3
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Pasik D, Frandsen BN, Meder M, Iyer S, Kurtén T, Myllys N. Gas-Phase Oxidation of Atmospherically Relevant Unsaturated Hydrocarbons by Acyl Peroxy Radicals. J Am Chem Soc 2024; 146:13427-13437. [PMID: 38712858 DOI: 10.1021/jacs.4c02523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
This study assesses the atmospheric impact of reactions between unsaturated hydrocarbons such as isoprene and monoterpenes and peroxy radicals containing various functional groups. We find that reactions between alkenes and acyl peroxy radicals have reaction rates high enough to be feasible in the atmosphere and lead to high molar mass accretion products. Moreover, the reaction between unsaturated hydrocarbons and acyl peroxy radicals leads to an alkyl radical, to which molecular oxygen rapidly adds. This finding is confirmed by both theoretical calculations and experiments. The formed perester peroxy radical may either undergo further H-shift reactions or react bimolecularly. The multifunctional oxygenated compounds formed through acyl peroxy radical + alkene reactions are potentially important contributors to particle formation and growth. Thus, acyl peroxy radical-initiated oxidation chemistry may need to be included in atmospheric models.
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Affiliation(s)
- Dominika Pasik
- Department of Chemistry, University of Helsinki, Helsinki 00014, Finland
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki 00014, Finland
| | - Benjamin N Frandsen
- Department of Chemistry, University of Helsinki, Helsinki 00014, Finland
- Aerosol Physics Laboratory, Tampere University, Tampere 33014, Finland
| | - Melissa Meder
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki 00014, Finland
| | - Siddharth Iyer
- Aerosol Physics Laboratory, Tampere University, Tampere 33014, Finland
| | - Theo Kurtén
- Department of Chemistry, University of Helsinki, Helsinki 00014, Finland
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki 00014, Finland
| | - Nanna Myllys
- Department of Chemistry, University of Helsinki, Helsinki 00014, Finland
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki 00014, Finland
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4
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Yang Y, Chen S, Zhang M, Shi Y, Luo J, Huang Y, Gu Z, Hu W, Zhang Y, He X, Yu C. Mesoporous nanoperforators as membranolytic agents via nano- and molecular-scale multi-patterning. Nat Commun 2024; 15:1891. [PMID: 38424084 PMCID: PMC10904871 DOI: 10.1038/s41467-024-46189-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
Plasma membrane lysis is an effective anticancer strategy, which mostly relying on soluble molecular membranolytic agents. However, nanomaterial-based membranolytic agents has been largely unexplored. Herein, we introduce a mesoporous membranolytic nanoperforators (MLNPs) via a nano- and molecular-scale multi-patterning strategy, featuring a spiky surface topography (nanoscale patterning) and molecular-level periodicity in the spikes with a benzene-bridged organosilica composition (molecular-scale patterning), which cooperatively endow an intrinsic membranolytic activity. Computational modelling reveals a nanospike-mediated multivalent perforation behaviour, i.e., multiple spikes induce nonlinearly enlarged membrane pores compared to a single spike, and that benzene groups aligned parallelly to a phospholipid molecule show considerably higher binding energy than other alignments, underpinning the importance of molecular ordering in phospholipid extraction for membranolysis. Finally, the antitumour activity of MLNPs is demonstrated in female Balb/c mouse models. This work demonstrates assembly of organosilica based bioactive nanostructures, enabling new understandings on nano-/molecular patterns co-governed nano-bio interaction.
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Affiliation(s)
- Yannan Yang
- Institute of Optoelectronics, Fudan University, Shanghai, 200433, China.
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.
- South Australian immunoGENomics Cancer Institute, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Shiwei Chen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Min Zhang
- Clinical Medicine Scientific and Technical Innovation Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200092, China.
| | - Yiru Shi
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jiangqi Luo
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yiming Huang
- Clinical Medicine Scientific and Technical Innovation Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200092, China
| | - Zhengying Gu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Wenli Hu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Ye Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China.
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China.
| | - Chengzhong Yu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China.
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5
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Daub CD, Kurtén T. Effect of an Electric Field on the Structure and Stability of Atmospheric Clusters. J Phys Chem A 2024; 128:646-655. [PMID: 38217515 DOI: 10.1021/acs.jpca.3c07260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
We study the influence of an applied electric field on the structure and stability of some common bimolecular clusters that are found in the atmosphere. These clusters play an important role in new particle formation (NPF). For low values of the electric field (i.e., |E| ≤ 0.01 V Å-1), we demonstrate that the field response of the clusters can be predicted from simply calculating the dipole moment of the cluster and the dipole moments of the constituent molecules and that the influence on the association energy of the cluster is minimal (i.e., <0.5 kcal mol-1). For higher field strengths |E| > 0.2 V Å-1, there can be more dramatic effects on both structure and energetics, as the induced dipole, charge transfer, and geometric distortion play a larger role. Although such large fields are not very relevant in the atmosphere, they do exist in some situations of experimental interest, such as near interfaces and in intense laser fields.
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Affiliation(s)
| | - Theo Kurtén
- Department of Chemistry, University of Helsinki, P.O. Box 55, Helsinki 00014, Finland
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6
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Pasik D, Iyer S, Myllys N. Cost-effective approach for atmospheric accretion reactions: a case of peroxy radical addition to isoprene. Phys Chem Chem Phys 2024; 26:2560-2567. [PMID: 38170853 DOI: 10.1039/d3cp04308h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
We present an accurate and cost-effective method for investigating the accretion reactions between unsaturated hydrocarbons and oxidized organic radicals. We use accretion between isoprene and primary, secondary and tertiary alkyl peroxy radicals as model reactions. We show that a systematic semiempirical transition state search can lead to better transition state structures than relaxed scanning with density functional theory with a significant gain in computational efficiency. Additionally, we suggest accurate and effective quantum chemical methods to study accretion reactions between large unsaturated hydrocarbons and oxidized organic radicals. Furthermore, we examine the atmospheric relevance of these types of reactions by calculating the bimolecular reaction rate coefficients and formation rates under atmospheric conditions from the quantum chemical reaction energy barriers.
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Affiliation(s)
- Dominika Pasik
- Department of Chemistry, University of Helsinki, Helsinki 00014, Finland.
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki 00014, Finland
| | - Siddharth Iyer
- Aerosol Physics Laboratory, Tampere University, Tampere FI-3720, Finland
| | - Nanna Myllys
- Department of Chemistry, University of Helsinki, Helsinki 00014, Finland.
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki 00014, Finland
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7
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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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8
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Knattrup Y, Kubečka J, Elm J. Nitric Acid and Organic Acids Suppress the Role of Methanesulfonic Acid in Atmospheric New Particle Formation. J Phys Chem A 2023; 127:7568-7578. [PMID: 37651638 DOI: 10.1021/acs.jpca.3c04393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Multicomponent atmospheric molecular clusters, typically comprising a combination of acids and bases, play a pivotal role in our climate system and contribute to the perplexing uncertainties embedded in modern climate models. Our understanding of cluster formation is limited by the lack of studies on complex mixed-acid-mixed-base systems. Here, we investigate multicomponent clusters consisting of mixtures of several acid and base molecules: sulfuric acid (SA), methanesulfonic acid (MSA), nitric acid (NA), formic acid (FA), along with methylamine (MA), dimethylamine (DMA), and trimethylamine (TMA). We calculated the binding free energies of a comprehensive set of 252 mixed-acid-mixed-base clusters at the DLPNO-CCSD(T0)/aug-cc-pVTZ//ωB97X-D/6-31++G(d,p) level of theory. Combined with the existing datasets, we simulated the new particle formation (NPF) rates using the Atmospheric Cluster Dynamics Code (ACDC). We find that the presence of NA and FA had a substantial impact, increasing the NPF rate by 60% at realistic conditions. Intriguingly, we find that NA and FA suppress the role of MSA in NPF. These findings suggest that even high concentration of MSA has a limited impact on NPF in polluted regions with high FA and NA. We outline a method for generating a lookup table that could potentially be used in climate models that sufficiently incorporates all the required chemistry. By unraveling the molecular mechanisms of mixed-acid-mixed-base clusters, we get one step closer to comprehending their implications for our global climate system.
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Affiliation(s)
- Yosef Knattrup
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jakub Kubečka
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department of Chemistry, iClimate, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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9
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Fomete S, Kubečka J, Elm J, Jen CN. Limited Role of Malonic Acid in Sulfuric Acid-Dimethylamine New Particle Formation. ACS OMEGA 2023; 8:19807-19815. [PMID: 37305259 PMCID: PMC10249388 DOI: 10.1021/acsomega.3c01643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/08/2023] [Indexed: 06/13/2023]
Abstract
Aerosols play an important role in climate and air quality; however, the mechanisms behind aerosol particle formation in the atmosphere are poorly understood. Studies have identified sulfuric acid, water, oxidized organics, and ammonia/amines as key precursors for forming aerosol particles in the atmosphere. Theoretical and experimental investigations have indicated that other species, such as organic acids, may be involved in atmospheric nucleation and growth of freshly formed aerosol particles. Organic acids, such as dicarboxylic acids, which are abundant in the atmosphere, have been measured in ultrafine aerosol particles. These observations suggest that organic acids may contribute to new particle formation in the atmosphere but their role remains ambiguous. This study examines how malonic acid interacts with sulfuric acid and dimethylamine to form new particles at warm boundary layer conditions using experimental observations from a laminar flow reactor and quantum chemical calculations coupled with cluster dynamics simulations. Observations reveal that malonic acid does not contribute to the initial steps (formation of <1 nm diameter particle) of nucleation with sulfuric acid-dimethylamine. In addition, malonic acid was found to not participate in the subsequent growth of the freshly nucleated 1 nm particles from sulfuric acid-dimethylamine reactions to diameters of 2 nm.
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Affiliation(s)
- Sandra
K.W. Fomete
- Department
of Chemical Engineering, Carnegie Mellon
University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Atmospheric Particle Studies, Carnegie
Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jakub Kubečka
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Coty N. Jen
- Department
of Chemical Engineering, Carnegie Mellon
University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Atmospheric Particle Studies, Carnegie
Mellon University, Pittsburgh, Pennsylvania 15213, United States
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10
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Toropainen A, Kangasluoma J, Vehkamäki H, Kubečka J. Heterogeneous Ion-Induced Nucleation of Water and Butanol Vapors Studied via Computational Quantum Chemistry beyond Prenucleation and Critical Cluster Sizes. J Phys Chem A 2023; 127:3976-3990. [PMID: 37126596 PMCID: PMC10184119 DOI: 10.1021/acs.jpca.3c00066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Water and butanol are used as working fluids in condensation particle counters, and condensation of a single vapor onto an ion can be used as a simple model system for the study of ion-induced nucleation in the atmosphere. Motivated by this, we examine heterogeneous nucleation of water (H2O) and n-butanol (BuOH) vapors onto three positively (Li+, Na+, K+) and three negatively charged (F-, Cl-, Br-) ions using classical nucleation theory and computational quantum chemistry methods. We study phenomena that cannot be captured by Kelvin-Thomson equation for small nucleation ion cores. Our quantum chemistry calculations reveal the molecular mechanism behind ion-induced nucleation for each studied system. Typically, ions become solvated from all sides after several vapor molecules condense onto the ion. However, we show that the clusters of water and large negatively charged ions (Cl- and Br-) thermodynamically prefer the ion being migrated to the cluster surface. Although our methods generally do not show clear sign-preference for ion-water nucleation, we identified positive sign-preference for ion-butanol nucleation caused by the possibility to form stabilizing hydrogen bonds between butanol molecules condensed onto a positively charged ion. These bonds cannot form when butanol condenses onto a negatively charged ion. Therefore, we show that ion charge, its sign, as well as vapor properties have effects on the prenucleation and critical cluster/droplet sizes and also on the molecular mechanism of ion-induced nucleation.
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Affiliation(s)
- Antti Toropainen
- University of Helsinki, Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, P.O. Box 64, Helsinki 00140, Finland
| | - Juha Kangasluoma
- University of Helsinki, Institute for Atmospheric and Earth System Research/Physics, 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
| | - Jakub Kubečka
- Aarhus University, Department of Chemistry, Langelandsgade 140, Aarhus 8000, Denmark
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11
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Patla A, Subramanian R. Thermodynamic and optical properties of HCOOH(H 2O) n and HCOOH(NH 3)(H 2O) (n-1) clusters at various temperatures and pressures: a computational study. Phys Chem Chem Phys 2023; 25:7869-7880. [PMID: 36857704 DOI: 10.1039/d2cp03908g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Density functional theory has been used to compute the gas-phase geometries, binding energies, ZPE-corrected binding energies, BSSE-corrected binding energies, binding enthalpies, and binding free energies of HCOOH(H2O)n and HCOOH(NH3)(H2O)(n-1) clusters with n = 1-8, 10, 12, 14, 16, 18, and 20. Enthalpies and free energies are calculated for a range of atmospherically relevant temperatures (T) and pressures (P) (from T = 298.15 K, P = 1013.25 hPa to T = 216.65 K, P = 226.32 hPa). The optical properties of those clusters have been studied at the CAM-B3LYP/aug-cc-pVDZ level of theory.
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Affiliation(s)
- Arnab Patla
- Department of Chemistry, Indian Institute of Technology Patna, 801103, India.
| | - Ranga Subramanian
- Department of Chemistry, Indian Institute of Technology Patna, 801103, India.
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12
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Ayoubi D, Knattrup Y, Elm J. Clusteromics V: Organic Enhanced Atmospheric Cluster Formation. ACS OMEGA 2023; 8:9621-9629. [PMID: 36936339 PMCID: PMC10018713 DOI: 10.1021/acsomega.3c00251] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Formic acid (FA) is a prominent candidate for organic enhanced nucleation due to its high abundance and stabilizing effect on smaller clusters. Its role in new particle formation is studied through the use of state-of-the-art quantum chemical methods on the cluster systems (acid)1-2(FA)1(base)1-2 with the acids being sulfuric acid (SA)/methanesulfonic acid (MSA) and the bases consisting of ammonia (A), methylamine (MA), dimethylamine (DMA), trimethylamine (TMA), and ethylenediamine (EDA). A funneling approach is used to determine the cluster structures with initial configurations generated through the ABCluster program, followed by semiempirical PM7 and ωB97X-D/6-31++G(d,p) calculations. The final binding free energy is calculated at the DLPNO-CCSD(T0)/aug-cc-pVTZ//ωB97X-D/6-31++G(d,p) level of theory using the quasi-harmonic approximation. Cluster dynamics simulations show that FA has a minuscule or negligible effect on the MSA-FA-base systems as well as most of the SA-FA-base systems. The SA-FA-DMA cluster system shows the highest influence from FA with an enhancement of 21%, compared to its non-FA counterpart.
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Affiliation(s)
- Daniel Ayoubi
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Yosef Knattrup
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department
of Chemistry, iClimate, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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13
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Kubečka J, Neefjes I, Besel V, Qiao F, Xie HB, Elm J. Atmospheric Sulfuric Acid-Multi-Base New Particle Formation Revealed through Quantum Chemistry Enhanced by Machine Learning. J Phys Chem A 2023; 127:2091-2103. [PMID: 36811954 DOI: 10.1021/acs.jpca.3c00068] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The formation of molecular clusters and secondary aerosols in the atmosphere has a significant impact on the climate. Studies typically focus on the new particle formation (NPF) of sulfuric acid (SA) with a single base molecule (e.g., dimethylamine or ammonia). In this work, we examine the combinations and synergy of several bases. Specifically, we used computational quantum chemistry to perform configurational sampling (CS) of (SA)0-4(base)0-4 clusters with five different types of bases: ammonia (AM), methylamine (MA), dimethylamine (DMA), trimethylamine (TMA), and ethylenediamine (EDA). Overall, we studied 316 different clusters. We used a traditional multilevel funnelling sampling approach augmented by a machine-learning (ML) step. The ML made the CS of these clusters possible by significantly enhancing the speed and quality of the search for the lowest free energy configurations. Subsequently, the cluster thermodynamics properties were evaluated at the DLPNO-CCSD(T0)/aug-cc-pVTZ//ωB97X-D/6-31++G(d,p) level of theory. The calculated binding free energies were used to evaluate the cluster stabilities for population dynamics simulations. The resultant SA-driven NPF rates and synergies of the studied bases are presented to show that DMA and EDA act as nucleators (although EDA becomes weak in large clusters), TMA acts as a catalyzer, and AM/MA is often overshadowed by strong bases.
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Affiliation(s)
- Jakub Kubečka
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Ivo Neefjes
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, P.O. Box 64, Helsinki 00140, Finland
| | - Vitus Besel
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, P.O. Box 64, Helsinki 00140, Finland
| | - Fukang Qiao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Hong-Bin Xie
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jonas Elm
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
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14
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Myllys N. The role of hydration in atmospheric salt particle formation. Phys Chem Chem Phys 2023; 25:7394-7400. [PMID: 36843365 DOI: 10.1039/d3cp00049d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
New-particle formation from condensable acid and base molecules is a ubiquitous phenomenon in the atmosphere. The role of water in salt particle formation is not fully understood as it can stabilize or destabilize cluster structures, which leads to non-linear effects on cluster formation dynamics. In the studied systems, increased relative humidity can enhance the particle formation for up to four orders of magnitude in the case of nitric acid, but it can also slightly reduce the particle formation in the cases of sulfuric acid and methanesulfonic acid. As the effect of relative humidity in salt particle formation varies many orders of magnitude depending on the acid and base molecules, neglecting hydration or using the same value for different systems may introduce remarkable inaccuracies in large-scale models.
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Affiliation(s)
- Nanna Myllys
- Department of Chemistry, University of Helsinki, Helsinki 00014, Finland. .,Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki 00014, Finland
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15
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Knattrup Y, Elm J. Clusteromics IV: The Role of Nitric Acid in Atmospheric Cluster Formation. ACS OMEGA 2022; 7:31551-31560. [PMID: 36092558 PMCID: PMC9453938 DOI: 10.1021/acsomega.2c04278] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Nitric acid (NA) has previously been shown to affect atmospheric new particle formation; however, its role still remains highly uncertain. Through the employment of state-of-the-art quantum chemical methods, we study the (acid)1-2(base)1-2 and (acid)3(base)2 clusters containing at least one nitric acid (NA) and sulfuric acid (SA) or methanesulfonic acid (MSA) with bases ammonia (A), methylamine (MA), dimethylamine (DMA), trimethylamine (TMA), and ethylenediamine (EDA). The initial cluster configurations are generated using the ABCluster program. PM7 and ωB97X-D/6-31++G(d,p) calculations are used to reduce the number of relevant configurations. The thermochemical parameters are calculated at the ωB97X-D/6-31++G(d,p) level of theory with the quasi-harmonic approximation, and the final single-point energies are calculated with high-level DLPNO-CCSD(T0)/aug-cc-pVTZ calculations. The enhancing effect from the presence of nitric acid on cluster formation is studied using the calculated thermochemical data and cluster dynamics simulations. We find that when NA is in excess compared with the other acids, it has a substantial enhancing effect on the cluster formation potential.
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Affiliation(s)
- Yosef Knattrup
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department
of Chemistry, iClimate, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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16
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Fomete SKW, Johnson JS, Myllys N, Jen CN. Experimental and Theoretical Study on the Enhancement of Alkanolamines on Sulfuric Acid Nucleation. J Phys Chem A 2022; 126:4057-4067. [PMID: 35729723 DOI: 10.1021/acs.jpca.2c01672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alkanolamines such as monoethanolamine (MEA), diethanolamine (DEA), and triethanolamine (TEA) are extensively used for CO2 capture and consumer products. Despite their prevalence in industrial applications, the fate of alkanolamines in the atmosphere remains relatively unknown. One likely reaction pathway for these chemicals in the atmosphere is new particle formation with sulfuric acid. Here, we present the first experimental results showing the formation of sulfuric acid dimers enhanced by MEA, DEA, and TEA from the measurement of molecular clusters. This study examines the nucleation reactions of MEA, DEA, and TEA with sulfuric acid in a clean, laminar flow reactor. The chemical compositions and concentrations of the freshly nucleated clusters were analyzed using a custom-built atmospheric pressure chemical ionization long time-of-flight mass spectrometer known as the Pittsburgh Cluster CIMS. Quantum chemical calculations and kinetic modeling of sulfuric acid-MEA/DEA/TEA clusters were also performed to determine relative cluster stabilities between these sulfuric acid-base systems. Experimental results indicate that MEA, DEA, and TEA at the part per trillion by volume (pptv) concentrations can enhance sulfuric acid dimer formation rates but to a lesser extent than dimethylamine (DMA). Thus, MEA, DEA, and TEA will potentially play an important role in new particle formation in industrial cities where these alkanolamines are emitted.
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Affiliation(s)
- Sandra K W Fomete
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.,Center for Atmospheric Particle Studies, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jack S Johnson
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.,Center for Atmospheric Particle Studies, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Nanna Myllys
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Coty N Jen
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.,Center for Atmospheric Particle Studies, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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17
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Elm J. Clusteromics III: Acid Synergy in Sulfuric Acid-Methanesulfonic Acid-Base Cluster Formation. ACS OMEGA 2022; 7:15206-15214. [PMID: 35572753 PMCID: PMC9089749 DOI: 10.1021/acsomega.2c01396] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/06/2022] [Indexed: 05/24/2023]
Abstract
Acid-base molecular clusters are an important stage in atmospheric new particle formation. While such clusters are most likely multicomponent in nature, there are very few reports on clusters consisting of multiple acid molecules and multiple base molecules. By applying state-of-the-art quantum chemical methods, we herein study electrically neutral (SA)1(MSA)1(base)0-2 clusters with base = ammonia (A), methylamine (MA), dimethylamine (DMA), trimethylamine (TMA) and ethylenediamine (EDA). The cluster structures are obtained using a funneling approach employing the ABCluster program, semiempirical PM7 calculations and ωB97X-D/6-31++G(d,p) calculations. The final binding free energies are calculated at the DLPNO-CCSD(T0)/aug-cc-pVTZ//ωB97X-D/6-31++G(d,p) level of theory using the quasi-harmonic approximation. Based on the calculated cluster geometries and thermochemistry (at 298.15 K and 1 atm), we find that the mixed (SA)1(MSA)1(base)1-2 clusters more resemble the (SA)2(base)1-2 clusters compared to the (MSA)2(base)1-2 clusters. Hence, some of the steric hindrance and lack of hydrogen bond capacity previously observed in the (MSA)2(base)1-2 clusters is diminished in the corresponding (SA)1(MSA)1(base)1-2 clusters. Cluster kinetics simulations reveal that the presence of an MSA molecule in the clusters enhances the cluster formation potential by up to a factor of 20. We find that the SA-MSA-DMA clusters have the highest cluster formation potential, and thus, this system should be further extended to larger sizes in future studies.
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18
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Becker D, Heitland J, Carlsson PTM, Elm J, Olenius T, Tödter S, Kharrazizadeh A, Zeuch T. Real-time monitoring of aerosol particle formation from sulfuric acid vapor at elevated concentrations and temperatures. Phys Chem Chem Phys 2022; 24:5001-5013. [PMID: 35142769 DOI: 10.1039/d1cp04580f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present study, time-resolved aerosol particle formation from sulfuric acid vapor is examined with special attention to the stabilization of molecular clusters in the early phase of unary nucleation. An important factor governing this process is the amount of condensable acid vapor. Here it is produced from fast gas-phase reactions in a batch-type reaction cell for which we introduce modifications enabling real-time monitoring. The key component for size- and time-resolved detection of ultrafine particles is a new 1 nm-SMPS. With this new tool at hand, the effect of varying the precursor concentration over two orders of magnitude is investigated. We demonstrate the ability to tune between different growth scenarios as indicated by the size-resolved particle traces which exhibit a transition from sigmoidal over quasi-stationary to peak-like shape. The second key parameter relevant for nucleation studies is the temperature-dependent cluster evaporation. Due to a temperature rise during the mixing stage of the experiment, evaporation is strongly promoted in the early phase. Therefore, the present study extends the T-range used in, e.g., smog chambers. We investigate this temperature effect in a kinetic simulation and can successfully combine simulated and measured data for validating theoretical evaporation rates obtained from DLPNO-CCSD(T0)-calculations.
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Affiliation(s)
- Daniel Becker
- Georg-August-Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany.
| | - Jonas Heitland
- Georg-August-Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany.
| | | | - Jonas Elm
- Aarhus Univerity, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Tinja Olenius
- Swedish Meteorological and Hydrological Institute, Air Quality Research Unit, Folkborgsvägen 17, SE-601 76 Norrköping, Sweden
| | - Sophia Tödter
- Georg-August-Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany.
| | - Amir Kharrazizadeh
- Georg-August-Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany.
| | - Thomas Zeuch
- Georg-August-Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany.
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19
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Zhou Y, Cao Q, Yang Y, Ma D, Zhu Q, Ma J. Effect of (H 2O) n ( n = 0–3, 13) on the NH 3 + OH reaction in the gas and liquid phases. RSC Adv 2022; 12:28010-28019. [PMID: 36320266 PMCID: PMC9524257 DOI: 10.1039/d2ra04931g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
We studied the effect of water clusters on the NH3 + OH reaction at both the DFT and CCSD(T) levels. The calculated rate constants for the pure reaction are 2.07 × 10−13 and 1.35 × 10−13 cm3 molecule−1 s−1 in the gas and liquid phases, respectively, and the gas-phase rate constants are consistent with the corresponding experimental result (1.70 × 10−13 cm3 molecule−1 s−1), while the liquid-phase rate constants are slightly smaller than the experimental value (5.84 × 10−12 cm3 molecule−1 s−1). In the gas phase, the presence of (H2O)n (n = 1–3) decreases the rate constant compared to the pure NH3 + OH reaction, and these results are in agreement with many reported H2O-catalyzed reactions. For the liquid phase reaction, compared with the case of n = 0–3, when the size of the water molecule cluster surrounding the OH radical is n = 13, the rate constant of the title reaction increases. Our study also shows that proton transfer is also a factor which accelerates the liquid phase NH3 + OH reaction. We used DFT and CCSD(T) methods with PCM solvation model to study the water cluster effect and solvation effect on the NH3 + OH reaction.![]()
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Affiliation(s)
- Yujie Zhou
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, 610065, China
| | - Qi Cao
- Reactor Operation and Application Research Sub-Institute, Nuclear Power Institute of China, Chengdu 610041, China
| | - Yu Yang
- Reactor Operation and Application Research Sub-Institute, Nuclear Power Institute of China, Chengdu 610041, China
| | - Dandan Ma
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, 610065, China
| | - Quan Zhu
- School of Chemical Engineering, Sichuan University, Chengdu, 610065, PR China
- Engineering Research Center of Combustion and Cooling for Aerospace Power, Ministry of Education, Sichuan University, Chengdu, 610065, PR China
| | - Jianyi Ma
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, 610065, China
- Engineering Research Center of Combustion and Cooling for Aerospace Power, Ministry of Education, Sichuan University, Chengdu, 610065, PR China
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20
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Myllys N, Myers D, Chee S, Smith JN. Molecular properties affecting the hydration of acid-base clusters. Phys Chem Chem Phys 2021; 23:13106-13114. [PMID: 34060578 DOI: 10.1039/d1cp01704g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the atmosphere, water in all phases is ubiquitous and plays important roles in catalyzing atmospheric chemical reactions, participating in cluster formation and affecting the composition of aerosol particles. Direct measurements of water-containing clusters are limited because water is likely to evaporate before detection, and therefore, theoretical tools are needed to study hydration in the atmosphere. We have studied thermodynamics and population dynamics of the hydration of different atmospherically relevant base monomers as well as sulfuric acid-base pairs. The hydration ability of a base seems to follow in the order of gas-phase base strength whereas hydration ability of acid-base pairs, and thus clusters, is related to the number of hydrogen binding sites. Proton transfer reactions at water-air interfaces are important in many environmental and biological systems, but a deeper understanding of their mechanisms remain elusive. By studying thermodynamics of proton transfer reactions in clusters containing up to 20 water molecules and a base molecule, we found that that the ability of a base to accept a proton in a water cluster is related to the aqueous-phase basicity. We also studied the second deprotonation reaction of a sulfuric acid in hydrated acid-base clusters and found that sulfate formation is most favorable in the presence of dimethylamine. Molecular properties related to the proton transfer ability in water clusters are discussed.
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Affiliation(s)
- Nanna Myllys
- Department of Chemistry, University of California, Irvine, California 92617, USA and Department of Chemistry, University of Jyväskylä, Jyväskylä 40014, Finland.
| | - Deanna Myers
- Department of Chemistry, University of California, Irvine, California 92617, USA
| | - Sabrina Chee
- Department of Chemistry, University of California, Irvine, California 92617, USA
| | - James N Smith
- Department of Chemistry, University of California, Irvine, California 92617, USA
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21
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Pal J, Patla A, Subramanian R. Thermodynamic properties of forming methanol-water and ethanol-water clusters at various temperatures and pressures and implications for atmospheric chemistry: A DFT study. CHEMOSPHERE 2021; 272:129846. [PMID: 33582505 DOI: 10.1016/j.chemosphere.2021.129846] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/25/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
The gas-phase geometries, binding energies, enthalpies, and free energies of methanol-(water)n and ethanol-(water)n clusters containing n=1-10,20,30,40, and 50 water molecules have been calculated using density functional theory. The binding energies are calculated at 0 K. The enthalpies are calculated at a temperature of 298.15 K and pressure of 1013.25 hPa (1 atm). The free energies are calculated at a wide range of temperature (T) and pressure (P) (from T = 298.15 K, P = 1013.25 hPa to T = 216.65 K, P = 226.32 hPa). The results show that the free energy of the formation of a specific cluster from its free molecules is negative (i.e., favorable) only below some critical temperature and pressure, which depends on the cluster's size. One of the most common volatile organic compounds (VOCs) in the troposphere is methanol, ethanol, and atmospheric aerosols containing methanol and ethanol. The Rayleigh scattering properties of methanol-water and ethanol-water clusters have been investigated. The scattering intensities were computed at static (∞ nm) and different wavelengths (700, 600, 500, and 400 nm) of naturally polarized light. Rayleigh scattering intensities increase about 9%-10% at 400 nm compared to the static limit (∞ nm) for both methanol-water and ethanol-water clusters.
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Affiliation(s)
- Jagannath Pal
- Department of Chemistry, Indian Institute of Technology Patna, 801103, India
| | - Arnab Patla
- Department of Chemistry, Indian Institute of Technology Patna, 801103, India
| | - Ranga Subramanian
- Department of Chemistry, Indian Institute of Technology Patna, 801103, India.
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22
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Kurfman LA, Odbadrakh TT, Shields GC. Calculating Reliable Gibbs Free Energies for Formation of Gas-Phase Clusters that Are Critical for Atmospheric Chemistry: (H 2SO 4) 3. J Phys Chem A 2021; 125:3169-3176. [PMID: 33825467 DOI: 10.1021/acs.jpca.1c00872] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effects of atmospheric aerosols on our climate are one of the biggest uncertainties in global climate models. Calculating the pathway for the formation of pre-nucleation clusters that become aerosols is challenging, requiring a comprehensive analysis of configurational space and highly accurate Gibbs free energy calculations. We identified a large set of minimum energy configurations of (H2SO4)3 using a sampling technique based on a genetic algorithm and a stepwise density functional theory (DFT) approach and computed the thermodynamics of formation of these configurations with more accurate wavefunction-based electronic energies computed on the DFT geometries. The DLPNO-CCSD(T) methods always return more positive energies compared to the DFT energies. Within the DLPNO-CCSD(T) methods, extrapolating to the complete basis set limit gives more positive free energies compared to explicitly correlated single-point energies. The CBS extrapolation was shown to be robust as both the 4-5 inverse polynomial and Riemann zeta function schemes were within chemical accuracy of one another.
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Affiliation(s)
- Luke A Kurfman
- Department of Chemistry, Furman University, Greenville, South Carolina 29613-0002, United States
| | - Tuguldur T Odbadrakh
- Department of Chemistry, Furman University, Greenville, South Carolina 29613-0002, United States
| | - George C Shields
- Department of Chemistry, Furman University, Greenville, South Carolina 29613-0002, United States
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23
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Rosati B, Christiansen S, Wollesen de Jonge R, Roldin P, Jensen MM, Wang K, Moosakutty SP, Thomsen D, Salomonsen C, Hyttinen N, Elm J, Feilberg A, Glasius M, Bilde M. New Particle Formation and Growth from Dimethyl Sulfide Oxidation by Hydroxyl Radicals. ACS EARTH & SPACE CHEMISTRY 2021; 5:801-811. [PMID: 33889792 PMCID: PMC8054244 DOI: 10.1021/acsearthspacechem.0c00333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 05/30/2023]
Abstract
Dimethyl sulfide (DMS) is produced by plankton in oceans and constitutes the largest natural emission of sulfur to the atmosphere. In this work, we examine new particle formation from the primary pathway of oxidation of gas-phase DMS by OH radicals. We particularly focus on particle growth and mass yield as studied experimentally under dry conditions using the atmospheric simulation chamber AURA. Experimentally, we show that aerosol mass yields from oxidation of 50-200 ppb of DMS are low (2-7%) and that particle growth rates (8.2-24.4 nm/h) are comparable with ambient observations. An HR-ToF-AMS was calibrated using methanesulfonic acid (MSA) to account for fragments distributed across both the organic and sulfate fragmentation table. AMS-derived chemical compositions revealed that MSA was always more dominant than sulfate in the secondary aerosols formed. Modeling using the Aerosol Dynamics, gas- and particle-phase chemistry kinetic multilayer model for laboratory CHAMber studies (ADCHAM) indicates that the Master Chemical Mechanism gas-phase chemistry alone underestimates experimentally observed particle formation and that DMS multiphase and autoxidation chemistry is needed to explain observations. Based on quantum chemical calculations, we conclude that particle formation from DMS oxidation in the ambient atmosphere will most likely be driven by mixed sulfuric acid/MSA clusters clustering with both amines and ammonia.
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Affiliation(s)
- Bernadette Rosati
- Department
of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, Vienna AT-1090, Austria
| | - Sigurd Christiansen
- Department
of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
| | | | - Pontus Roldin
- Division
of Nuclear Physics, Lund University, P.O. Box 118, Lund SE-221
00, Sweden
| | - Mads Mørk Jensen
- Department
of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
| | - Kai Wang
- Department
of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
| | - Shamjad P. Moosakutty
- Department
of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
- Clean Combustion
Research Center, King Abdullah University
of Science and Technology, Thuwal KSA-23955, Saudi Arabia
| | - Ditte Thomsen
- Department
of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
| | - Camilla Salomonsen
- Department
of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
| | - Noora Hyttinen
- Nano
and Molecular Systems Research Unit, University
of Oulu, P.O. Box 3000, Oulu FI-90014, Finland
- Department
of Applied Physics, University of Eastern
Finland, P.O. Box 1627, Kuopio FI-70211, Finland
| | - Jonas Elm
- Department
of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
| | - Anders Feilberg
- Department
of Biological and Chemical Engineering, Aarhus University, Finlandsgade
12, Aarhus N DK-8200, Denmark
| | - Marianne Glasius
- Department
of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
| | - Merete Bilde
- Department
of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C DK-8000, Denmark
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24
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Pal J, Teja PS, Subramanian R. Sodium and lithium ions in aerosol: thermodynamic and rayleigh light scattering properties. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02683-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Besel V, Kubečka J, Kurtén T, Vehkamäki H. Impact of Quantum Chemistry Parameter Choices and Cluster Distribution Model Settings on Modeled Atmospheric Particle Formation Rates. J Phys Chem A 2020; 124:5931-5943. [PMID: 32568535 DOI: 10.1021/acs.jpca.0c03984] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We tested the influence of various parameters on the new particle formation rate predicted for the sulfuric acid-ammonia system using quantum chemistry and cluster distribution dynamics simulations, in our case, Atmospheric Cluster Dynamics Code (ACDC). We found that consistent consideration of the rotational symmetry number of monomers (sulfuric acid and ammonia molecules, and bisulfate and ammonium ions) leads to a significant rise in the predicted particle formation rate, whereas inclusion of the rotational symmetry number of the clusters only changes the results slightly, and only in conditions where charged clusters dominate the particle formation rate. This is because most of the clusters stable enough to participate in new particle formation have a rotational symmetry number of 1, and few exceptions to this rule are positively charged clusters. In contrast, the application of the quasi-harmonic correction for low-frequency vibrational modes tends to generally decrease predicted new particle formation rates and also significantly alters the slope of the formation rate curve plotted against the sulfuric acid concentration, which is a typical convention in atmospheric aerosol science. The impact of the maximum size of the clusters explicitly included in the simulations depends on the simulated conditions. The errors arising from a limited set of clusters are higher for higher evaporation rates, and thus tend to increase with temperature. Similarly, the errors tend to be higher for lower vapor concentrations. The boundary conditions for outgrowing clusters (that are counted as formed particles) have only a small influence on the results, provided that the definition is chemically reasonable and that the set of simulated clusters is sufficiently large. A comparison with data from the Cosmics Leaving OUtdoor Droplets (CLOUD) chamber and a cluster distribution dynamics model using older quantum chemistry input data shows improved agreement when using our new input data and the proposed combination of symmetry and quasi-harmonic corrections.
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Affiliation(s)
- Vitus Besel
- University of Helsinki, Physicum, Gustaf Hällströmin Katu 2, 00560 Helsinki, Finland
| | - Jakub Kubečka
- University of Helsinki, Physicum, Gustaf Hällströmin Katu 2, 00560 Helsinki, Finland
| | - Theo Kurtén
- University of Helsinki, Chemicum, A. I. Virtasen aukio 1, 00560 Helsinki, Finland
| | - Hanna Vehkamäki
- University of Helsinki, Physicum, Gustaf Hällströmin Katu 2, 00560 Helsinki, Finland
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26
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Rasmussen FR, Kubečka J, Besel V, Vehkamäki H, Mikkelsen KV, Bilde M, Elm J. Hydration of Atmospheric Molecular Clusters III: Procedure for Efficient Free Energy Surface Exploration of Large Hydrated Clusters. J Phys Chem A 2020; 124:5253-5261. [DOI: 10.1021/acs.jpca.0c02932] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Jakub Kubečka
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki FI-00014, Finland
| | - Vitus Besel
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki FI-00014, Finland
| | - Hanna Vehkamäki
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki FI-00014, Finland
| | - Kurt V. Mikkelsen
- Department of Chemistry, University of Copenhagen, Universitetesparken 5, 2100 Copenhagen, Denmark
| | - Merete Bilde
- Department of Chemistry and iClimate, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Jonas Elm
- Department of Chemistry and iClimate, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
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27
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Schmitz G, Elm J. Assessment of the DLPNO Binding Energies of Strongly Noncovalent Bonded Atmospheric Molecular Clusters. ACS OMEGA 2020; 5:7601-7612. [PMID: 32280904 PMCID: PMC7144154 DOI: 10.1021/acsomega.0c00436] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/11/2020] [Indexed: 05/03/2023]
Abstract
This work assesses the performance of DLPNO-CCSD(T0), DLPNO-MP2, and density functional theory methods in calculating the binding energies of a representative test set of 45 atmospheric acid-acid, acid-base, and acid-water dimer clusters. The performance of the approximate methods is compared to high level explicitly correlated CCSD(F12*)(T)/complete basis set (CBS) reference calculations. Out of the tested density functionals, ωB97X-D3(BJ) shows the best performance with a mean deviation of 0.09 kcal/mol and a maximum deviation of 0.83 kcal/mol. The RI-CC2/aug-cc-pV(T+d)Z level of theory severely overpredicts the cluster binding energies with a mean deviation of -1.31 kcal/mol and a maximum deviation up to -3.00 kcal/mol. Hence, RI-CC2/aug-cc-pV(T+d)Z should not be utilized for studying atmospheric molecular clusters. The DLPNO variants are tested both with and without the inclusion of explicit correlation (F12) in the wavefunction, with different pair natural orbital (PNO) settings (loosePNO, normalPNO, and tightPNO) and using both double and triple zeta basis sets. The performance of the DLPNO-MP2 methods is found to be independent of PNO settings and yield low mean deviations of -0.84 kcal/mol or below. However, DLPNO-MP2 requires explicitly correlated wavefunctions to yield maximum deviations below 1.40 kcal/mol. For obtaining high accuracy, with maximum deviation below ∼1.0 kcal/mol, either DLPNO-CCSD(T0)/aug-cc-pVTZ (normalPNO) calculations or DLPNO-CCSD(T0)-F12/cc-pVTZ-F12 (normalPNO) calculations are required. The most accurate level of theory is found to be DLPNO-CCSD(T0)-F12/cc-pVTZ-F12 using a tightPNO criterion which yields a mean deviation of 0.10 kcal/mol, with a maximum deviation of 0.20 kcal/mol, compared to the CCSD(F12*)(T)/CBS reference.
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Affiliation(s)
- Gunnar Schmitz
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department
of Chemistry and iClimate, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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28
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Li D, Chen D, Liu F, Wang W. Role of glycine on sulfuric acid-ammonia clusters formation: Transporter or participator. J Environ Sci (China) 2020; 89:125-135. [PMID: 31892385 DOI: 10.1016/j.jes.2019.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/07/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
Glycine (Gly) is ubiquitous in the atmosphere and plays a vital role in new particle formation (NPF). However, the potential mechanism of its on sulfuric acid (SA) - ammonia (A) clusters formation under various atmospheric conditions is still ambiguous. Herein, a (Gly)x·(SA)y·(A)z (z ≤ x + y ≤ 3) multicomponent system was investigated by using density functional theory (DFT) combined with Atmospheric Cluster Dynamics Code (ACDC) at different temperatures and precursor concentrations. The results show that Gly, with one carboxyl (-COOH) and one amine (-NH2) group, can interact strongly with SA and A in two directions through hydrogen bonds or proton transfer. Within the relevant range of atmospheric concentrations, Gly can enhance the formation rate of SA-A-based clusters, especially at low temperature, low [SA], and median [A]. The enhancement (R) of Gly on NPF can be up to 340 at T = 218.15 K, [SA] = 104, [A] = 109, and [Gly] = 107 molecules/cm3. In addition, the main growth paths of clusters show that Gly molecules participate into cluster formation in the initial stage and eventually leave the cluster by evaporation in subsequent cluster growth at low [Gly], it acts as an important "transporter" to connect the smaller and larger cluster. With the increase of [Gly], it acts as a "participator" directly participating in NPF.
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Affiliation(s)
- Danfeng Li
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Dongping Chen
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Fengyi Liu
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Wenliang Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
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29
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Enhancing Potential of Trimethylamine Oxide on Atmospheric Particle Formation. ATMOSPHERE 2019. [DOI: 10.3390/atmos11010035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The role of an oxidation product of trimethylamine, trimethylamine oxide, in atmospheric particle formation is studied using quantum chemical methods and cluster formation simulations. Molecular-level cluster formation mechanisms are resolved, and theoretical results on particle formation are confirmed with mass spectrometer measurements. Trimethylamine oxide is capable of forming only one hydrogen bond with sulfuric acid, but unlike amines, trimethylamine oxide can form stable clusters via ion–dipole interactions. That is because of its zwitterionic structure, which causes a high dipole moment. Cluster growth occurs close to the acid:base ratio of 1:1, which is the same as for other monoprotic bases. Enhancement potential of trimethylamine oxide in particle formation is much higher than that of dimethylamine, but lower compared to guanidine. Therefore, at relatively low concentrations and high temperatures, guanidine and trimethylamine oxide may dominate particle formation events over amines.
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30
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Kubečka J, Besel V, Kurtén T, Myllys N, Vehkamäki H. Configurational Sampling of Noncovalent (Atmospheric) Molecular Clusters: Sulfuric Acid and Guanidine. J Phys Chem A 2019; 123:6022-6033. [PMID: 31273989 DOI: 10.1021/acs.jpca.9b03853] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We studied the configurational sampling of noncovalently bonded molecular clusters relevant to the atmosphere. In this article, we discuss possible approaches to searching for optimal configurations and present one alternative based on systematic configurational sampling, which seems able to overcome the typical problems associated with searching for global minima on multidimensional potential energy surfaces. Since atmospheric molecular clusters are usually held together by intermolecular bonds, we also present a cost-effective strategy for treating hydrogen bonding and proton transferring by using rigid molecules and ions in different protonation states and illustrate its performance on clusters containing guanidine and sulfuric acid.
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Affiliation(s)
- Jakub Kubečka
- Institute for Atmospheric and Earth System Research , University of Helsinki , Helsinki FI-00014 , Finland
| | - Vitus Besel
- Institute for Atmospheric and Earth System Research , University of Helsinki , Helsinki FI-00014 , Finland
| | - Theo Kurtén
- Institute for Atmospheric and Earth System Research , University of Helsinki , Helsinki FI-00014 , Finland
| | - Nanna Myllys
- Department of Chemistry , University of California , Irvine , California 92697-2025 , United States
| | - Hanna Vehkamäki
- Institute for Atmospheric and Earth System Research , University of Helsinki , Helsinki FI-00014 , Finland
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31
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Chee S, Myllys N, Barsanti KC, Wong BM, Smith JN. An Experimental and Modeling Study of Nanoparticle Formation and Growth from Dimethylamine and Nitric Acid. J Phys Chem A 2019; 123:5640-5648. [DOI: 10.1021/acs.jpca.9b03326] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sabrina Chee
- Department of Chemistry, University of California, Irvine, California 92617, United States
| | - Nanna Myllys
- Department of Chemistry, University of California, Irvine, California 92617, United States
| | | | | | - James N. Smith
- Department of Chemistry, University of California, Irvine, California 92617, United States
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32
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Elm J. Unexpected Growth Coordinate in Large Clusters Consisting of Sulfuric Acid and C8H12O6 Tricarboxylic Acid. J Phys Chem A 2019; 123:3170-3175. [DOI: 10.1021/acs.jpca.9b00428] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jonas Elm
- Department of Chemistry and iClimate, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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33
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Myllys N, Chee S, Olenius T, Lawler M, Smith J. Molecular-Level Understanding of Synergistic Effects in Sulfuric Acid–Amine–Ammonia Mixed Clusters. J Phys Chem A 2019; 123:2420-2425. [DOI: 10.1021/acs.jpca.9b00909] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nanna Myllys
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Sabrina Chee
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Tinja Olenius
- Department of Environmental Science and Analytical Chemistry & Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Michael Lawler
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - James Smith
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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34
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Luccarelli J, Paton RS. Hydrogen-Bond-Dependent Conformational Switching: A Computational Challenge from Experimental Thermochemistry. J Org Chem 2019; 84:613-621. [PMID: 30586500 DOI: 10.1021/acs.joc.8b02436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have compiled an experimental data set (SWITCH10) of equilibrium constants for a series of hydrogen-bond-dependent conformational switches. These organic molecules possess common functionalities and are representative in terms of size and composition of systems routinely studied computationally. They exist as two well-defined conformations which serve as a useful tool to benchmark computational estimates of experimental Gibbs energy differences. We examine the performance of HF theory and a variety of density functionals (B3LYP, B3LYP-D3, CAM-B3LYP, ωB97X-D, M06-2X) against these experimental benchmarks. Surprisingly, despite a strong similarity between the two switch conformations, the average errors (0.4-1.7 kcal·mol-1) obtained across the data set for all methods are larger than obtained with HF calculations. B3LYP was found to outperform implicitly and explicitly dispersion-corrected functionals, with an average error smaller by 1 kcal·mol-1. Unsystematic errors in the optimized structures were found to contribute to the relatively poor performance obtained, while quasi-rigid rotor harmonic oscillator thermal contributions are important in improving the accuracy of computed Gibbs energy differences. These results emphasize the challenge of quantitative accuracy in computing solution-phase thermochemistry for flexible systems and caution against the often used (but unstated) assumption of favorable error cancellation in comparing conformers or stereoisomers.
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Affiliation(s)
- James Luccarelli
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , U.K.,Department of Psychiatry , Massachusetts General Hospital , 55 Fruit Street , Boston , Massachusetts 02114 , United States
| | - Robert S Paton
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , U.K.,Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
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35
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Joranger T, Kildgaard JV, Jørgensen S, Elm J, Mikkelsen KV. Benchmarking sampling methodology for calculations of Rayleigh light scattering properties of atmospheric molecular clusters. Phys Chem Chem Phys 2019; 21:17274-17287. [DOI: 10.1039/c9cp02573a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We present four different computational methods for benchmarking the sampling and Rayleigh light scattering of hydrogen bonded atmospheric molecular clusters.
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Affiliation(s)
- Teis Joranger
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen Ø
- Denmark
| | | | - Solvejg Jørgensen
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen Ø
- Denmark
| | - Jonas Elm
- Department of Chemistry and iClimate
- Aarhus University
- 8000 Århus C
- Denmark
| | - Kurt V. Mikkelsen
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen Ø
- Denmark
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36
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Kildgaard JV, Mikkelsen KV, Bilde M, Elm J. Hydration of Atmospheric Molecular Clusters II: Organic Acid–Water Clusters. J Phys Chem A 2018; 122:8549-8556. [DOI: 10.1021/acs.jpca.8b07713] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jens Vive Kildgaard
- Department of Energy Conversion and Storage, DTU Energy, 2800 Kgs. Lyngby, Denmark
| | - Kurt V. Mikkelsen
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Merete Bilde
- Department of Chemistry and iClimate, Aarhus University, 8000 Aarhus, Denmark
| | - Jonas Elm
- Department of Chemistry and iClimate, Aarhus University, 8000 Aarhus, Denmark
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37
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Myllys N, Ponkkonen T, Passananti M, Elm J, Vehkamäki H, Olenius T. Guanidine: A Highly Efficient Stabilizer in Atmospheric New-Particle Formation. J Phys Chem A 2018; 122:4717-4729. [PMID: 29693391 DOI: 10.1021/acs.jpca.8b02507] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of a strong organobase, guanidine, in sulfuric acid-driven new-particle formation is studied using state-of-the-art quantum chemical methods and molecular cluster formation simulations. Cluster formation mechanisms at the molecular level are resolved, and theoretical results on cluster stability are confirmed with mass spectrometer measurements. New-particle formation from guanidine and sulfuric acid molecules occurs without thermodynamic barriers under studied conditions, and clusters are growing close to a 1:1 composition of acid and base. Evaporation rates of the most stable clusters are extremely low, which can be explained by the proton transfers and symmetrical cluster structures. We compare the ability of guanidine and dimethylamine to enhance sulfuric acid-driven particle formation and show that more than 2000-fold concentration of dimethylamine is needed to yield as efficient particle formation as in the case of guanidine. At similar conditions, guanidine yields 8 orders of magnitude higher particle formation rates compared to dimethylamine. Highly basic compounds such as guanidine may explain experimentally observed particle formation events at low precursor vapor concentrations, whereas less basic and more abundant bases such as ammonia and amines are likely to explain measurements at high concentrations.
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Affiliation(s)
- Nanna Myllys
- Institute for Atmospheric and Earth System Research/Physics , University of Helsinki , P.O. Box 64, 00014 Helsinki , Finland
| | - Tuomo Ponkkonen
- Institute for Atmospheric and Earth System Research/Physics , University of Helsinki , P.O. Box 64, 00014 Helsinki , Finland
| | - Monica Passananti
- Institute for Atmospheric and Earth System Research/Physics , University of Helsinki , P.O. Box 64, 00014 Helsinki , Finland
| | - Jonas Elm
- Department of Chemistry and iClimate , Aarhus University , Langelandsgade 140 , DK-8000 Aarhus , Denmark
| | - Hanna Vehkamäki
- Institute for Atmospheric and Earth System Research/Physics , University of Helsinki , P.O. Box 64, 00014 Helsinki , Finland
| | - Tinja Olenius
- Department of Environmental Science and Analytical Chemistry and Bolin Centre for Climate Research , Stockholm University , Svante Arrhenius väg 8 , SE-114 18 Stockholm , Sweden
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38
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Kildgaard JV, Mikkelsen KV, Bilde M, Elm J. Hydration of Atmospheric Molecular Clusters: A New Method for Systematic Configurational Sampling. J Phys Chem A 2018; 122:5026-5036. [PMID: 29741906 DOI: 10.1021/acs.jpca.8b02758] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a new systematic configurational sampling algorithm for investigating the potential energy surface of hydrated atmospheric molecular clusters. The algorithm is based on creating a Fibonacci sphere around each atom in the cluster and adding water molecules to each point in nine different orientations. For the sampling of water molecules to existing hydrogen bonds, the cluster is displaced along the hydrogen bond, and a water molecule is placed in between in three different orientations. Generated redundant structures are eliminated based on minimizing the root-mean-square distance of different conformers. Initially, the clusters are sampled using the semiempirical PM6 method and subsequently using density functional theory (M06-2X and ωB97X-D) with the 6-31++G(d,p) basis set. Applying the developed algorithm, we study the hydration of sulfuric acid with up to 15 water molecules. We find that the addition of the first four water molecules "saturate" the sulfuric acid molecule and that they are more thermodynamically favorable than the addition of water molecules 5-15. Using the large generated set of conformers, we assess the performance of approximate methods (ωB97X-D, M06-2X, PW91, and PW6B95-D3) in calculating the binding energies and assigning the global minimum conformation compared to high level CCSD(T)-F12a/VDZ-F12 reference calculations. The tested DFT functionals systematically overestimate the binding energies compared to coupled cluster calculations, and we find that this deficiency can be corrected by a simple scaling factor.
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Affiliation(s)
| | - Kurt V Mikkelsen
- Department of Chemistry , University of Copenhagen , Copenhagen , Denmark
| | - Merete Bilde
- Department of Chemistry and iClimate , Aarhus University , Aarhus , Denmark
| | - Jonas Elm
- Department of Chemistry and iClimate , Aarhus University , Aarhus , Denmark
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39
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Song G, Bozzelli JW. Structural and thermochemical properties of methyl ethyl sulfide alcohols: HOCH 2
SCH 2
CH 3
, CH 3
SCH(OH)CH 3
, CH 3
SCH 2
CH 2
OH, and radicals corresponding to loss of H atom. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Guanghui Song
- Department of Chemical, Biological and Pharmaceutical Engineering; New Jersey Institute of Technology, University Heights; Newark NJ USA
| | - Joseph W. Bozzelli
- Department of Chemical, Biological and Pharmaceutical Engineering; New Jersey Institute of Technology, University Heights; Newark NJ USA
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40
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Hirvonen V, Myllys N, Kurtén T, Elm J. Closed-Shell Organic Compounds Might Form Dimers at the Surface of Molecular Clusters. J Phys Chem A 2018; 122:1771-1780. [PMID: 29364673 DOI: 10.1021/acs.jpca.7b11970] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of covalently bound dimer formation is studied using high-level quantum chemical methods. Reaction free energy profiles for dimer formation between common oxygen-containing functional groups are calculated, and based on the Gibbs free energy differences between transition states and reactants, we show that none of the studied two-component gas-phase reactions are kinetically feasible at 298.15 K and 1 atm. Therefore, the catalyzing effect of water, base, or acid molecules is calculated, and sulfuric acid is identified to lower the activation free energies significantly. We find that the reactions yielding hemiacetal, peroxyhemiacetal, α-hydroxyester, and geminal diol products occur with activation free energies of less than 10 kcal/mol with sulfuric acid as a catalyst, indicating that these reactions could potentially take place on the surface of sulfuric acid clusters. Additionally, the formed dimer products bind stronger onto the pre-existing cluster than the corresponding reagent monomers do. This implies that covalent dimerization reactions stabilize the existing cluster thermodynamically and make it less likely to evaporate. However, the studied small organic compounds, which contain only one functional group, are not able to form dimer products that are stable against evaporation at atmospheric conditions. Calculations of dimer formation onto a cluster surface and the clustering ability of dimer products should be extended to large terpene oxidation products in order to estimate the real atmospheric significance.
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Affiliation(s)
- Viivi Hirvonen
- Department of Physics, University of Helsinki , 00100 Helsinki, Finland
| | - Nanna Myllys
- Department of Physics, University of Helsinki , 00100 Helsinki, Finland
| | - Theo Kurtén
- Department of Chemistry, University of Helsinki , 00100 Helsinki, Finland
| | - Jonas Elm
- Department of Chemistry, Aarhus University , 8000 Aarhus C, Denmark
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41
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Besora M, Vidossich P, Lledós A, Ujaque G, Maseras F. Calculation of Reaction Free Energies in Solution: A Comparison of Current Approaches. J Phys Chem A 2018; 122:1392-1399. [DOI: 10.1021/acs.jpca.7b11580] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria Besora
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Catalonia, Spain
| | - Pietro Vidossich
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Valles, Catalonia, Spain
- COBO
Computational Bio-Organic Chemistry Bogotá, Department of Chemistry, Universidad de los Andes, Carrera 1 No. 18A 10, 111711 Bogotá, Colombia
| | - Agustí Lledós
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Valles, Catalonia, Spain
| | - Gregori Ujaque
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Valles, Catalonia, Spain
| | - Feliu Maseras
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Catalonia, Spain
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Valles, Catalonia, Spain
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42
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Elm J. Elucidating the Limiting Steps in Sulfuric Acid–Base New Particle Formation. J Phys Chem A 2017; 121:8288-8295. [DOI: 10.1021/acs.jpca.7b08962] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jonas Elm
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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43
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Elm J, Passananti M, Kurtén T, Vehkamäki H. Diamines Can Initiate New Particle Formation in the Atmosphere. J Phys Chem A 2017; 121:6155-6164. [DOI: 10.1021/acs.jpca.7b05658] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonas Elm
- Department
of Chemistry, Aarhus University, Aarhus 8000, Denmark
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44
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Myllys N, Olenius T, Kurtén T, Vehkamäki H, Riipinen I, Elm J. Effect of Bisulfate, Ammonia, and Ammonium on the Clustering of Organic Acids and Sulfuric Acid. J Phys Chem A 2017; 121:4812-4824. [DOI: 10.1021/acs.jpca.7b03981] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nanna Myllys
- Department
of Physics, University of Helsinki, Helsinki FI-00014, Finland
| | - Tinja Olenius
- Department of Environmental Science and Analytical Chemistry & Bolin Centre for Climate Research, Stockholm University, 106 91 Stockholm, Sweden
| | - Theo Kurtén
- Department
of Chemistry, University of Helsinki, Helsinki FI-00014, Finland
| | - Hanna Vehkamäki
- Department
of Physics, University of Helsinki, Helsinki FI-00014, Finland
| | - Ilona Riipinen
- Department of Environmental Science and Analytical Chemistry & Bolin Centre for Climate Research, Stockholm University, 106 91 Stockholm, Sweden
| | - Jonas Elm
- Department
of Physics, University of Helsinki, Helsinki FI-00014, Finland
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45
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Elm J, Myllys N, Kurtén T. What Is Required for Highly Oxidized Molecules To Form Clusters with Sulfuric Acid? J Phys Chem A 2017; 121:4578-4587. [DOI: 10.1021/acs.jpca.7b03759] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jonas Elm
- Department
of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Nanna Myllys
- Department
of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Theo Kurtén
- Department
of Chemistry, University of Helsinki, FI-00014 Helsinki, Finland
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Studziński W, Gackowska A, Przybyłek M, Gaca J. Studies on the formation of formaldehyde during 2-ethylhexyl 4-(dimethylamino)benzoate demethylation in the presence of reactive oxygen and chlorine species. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:8049-8061. [PMID: 28133704 PMCID: PMC5384958 DOI: 10.1007/s11356-017-8477-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
In order to protect the skin from UV radiation, personal care products (PCPS) often contain chemical UV-filters. These compounds can enter the environment causing serious consequences on the water ecosystems. The aim of this study was to examine, the effect of different factors, such as UV light, the presence of NaOCl and H2O2 on the formaldehyde formation during popular UV filter, 2-ethylhexyl 4-(dimethylamino)benzoate (ODPABA) demethylation. The concentration of formaldehyde was determined by VIS spectrophotometry after derivatization. The reaction mixtures were qualitatively analyzed using GC/MS chromatography. The highest concentration of formaldehyde was observed in the case of ODPABA/H2O2/UV reaction mixture. In order to describe two types of demethylation mechanisms, namely, radical and ionic, the experimental results were enriched with Fukui function analysis and thermodynamic calculations. In the case of non-irradiated system containing ODPABA and NaOCl, demethylation reaction probably proceeds via ionic mechanism. As it was established, amino nitrogen atom in the ODPABA molecule is the most susceptible site for the HOCl electrophilic attack, which is the first step of ionic demethylation mechanism. In the case of irradiated mixtures, the reaction is probably radical in nature. The results of thermodynamic calculations showed that abstraction of the hydrogen from N(CH3)2 group is more probable than from 2-ethylhexyl moiety, which indicates higher susceptibility of N(CH3)2 to the oxidation.
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Affiliation(s)
- Waldemar Studziński
- Faculty of Chemical Technology and Engineering, University of Technology and Life Sciences, Seminaryjna 3, 85-326, Bydgoszcz, Poland
| | - Alicja Gackowska
- Faculty of Chemical Technology and Engineering, University of Technology and Life Sciences, Seminaryjna 3, 85-326, Bydgoszcz, Poland
| | - Maciej Przybyłek
- Department of Physical Chemistry, Faculty of Pharmacy, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Kurpińskiego 5, 85-950, Bydgoszcz, Poland.
| | - Jerzy Gaca
- Faculty of Chemical Technology and Engineering, University of Technology and Life Sciences, Seminaryjna 3, 85-326, Bydgoszcz, Poland
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Elm J, Myllys N, Olenius T, Halonen R, Kurtén T, Vehkamäki H. Formation of atmospheric molecular clusters consisting of sulfuric acid and C8H12O6 tricarboxylic acid. Phys Chem Chem Phys 2017; 19:4877-4886. [DOI: 10.1039/c6cp08127d] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the structures and thermochemical properties of (MBTCA)1−3(H2SO4)1−4 atmospheric molecular clusters.
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Affiliation(s)
- Jonas Elm
- Division of Atmospheric Sciences
- Department of Physics
- University of Helsinki
- FI-00014 Helsinki
- Finland
| | - Nanna Myllys
- Division of Atmospheric Sciences
- Department of Physics
- University of Helsinki
- FI-00014 Helsinki
- Finland
| | - Tinja Olenius
- Department of Environmental Science and Analytical Chemistry (ACES) and Bolin Centre for Climate Research
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Roope Halonen
- Division of Atmospheric Sciences
- Department of Physics
- University of Helsinki
- FI-00014 Helsinki
- Finland
| | - Theo Kurtén
- Department of Chemistry
- University of Helsinki
- FI-00014 Helsinki
- Finland
| | - Hanna Vehkamäki
- Division of Atmospheric Sciences
- Department of Physics
- University of Helsinki
- FI-00014 Helsinki
- Finland
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