Articles | Volume 18, issue 22
https://doi.org/10.5194/gmd-18-9189-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/gmd-18-9189-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Model description paper
| 
28 Nov 2025
Model description paper |
| 28 Nov 2025
| 28 Nov 2025
VaPOrS v1.0.1: an automated model for functional group detection and property prediction of organic compounds via SMILES notation
Mojtaba Bezaatpour
CORRESPONDING AUTHOR
Aerosol Physics Laboratory, Tampere University, 33720 Tampere, Finland
Miikka Dal Maso
Aerosol Physics Laboratory, Tampere University, 33720 Tampere, Finland
Aerosol Physics Laboratory, Tampere University, 33720 Tampere, Finland
Department of Chemistry, University of Helsinki, 00014 Helsinki, Finland
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Shawon Barua, Avinash Kumar, Prasenjit Seal, Siddharth Iyer, and Matti Rissanen
EGUsphere, https://doi.org/10.5194/egusphere-2025-5207, https://doi.org/10.5194/egusphere-2025-5207, 2025
This preprint is open for discussion and under review for Atmospheric Chemistry and Physics (ACP).
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This work illustrates how long chain linear aldehydes have the potential to undergo atmospheric autoxidation and lead to prompt formation of condensable material which subsequently contributes to aerosol formation, deteriorating the air quality of urban atmospheres. We performed laboratory experiments using state-of-the-art mass spectrometry technique combined with a flow reactor under atmospheric conditions to resolve the autoxidation mechanism of n-aldehydes initiated by a common oxidant.
Teemu Lepistö, Hilkka Timonen, Topi Rönkkö, and Miikka Dal Maso
EGUsphere, https://doi.org/10.5194/egusphere-2025-4339, https://doi.org/10.5194/egusphere-2025-4339, 2025
This preprint is open for discussion and under review for Atmospheric Chemistry and Physics (ACP).
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Condensation of vapour molecules onto aerosol particles is a key process regarding aerosol health and climate effects. The condensation sink (CS) estimates the attachment rate of vapour molecules onto existing particles. Here, we explore the concept of size-resolved CS as many of the effects related to condensation are dependent on the size of the existing particles. Our results show clear location-dependent differences in the CS size distributions which may have not been considered before.
Neil M. Donahue, Victoria Hofbauer, Henning Finkenzeller, Dominik Stolzenburg, Paulus S. Bauer, Randall Chiu, Lubna Dada, Jonathan Duplissy, Xu-Cheng He, Martin Heinritzi, Christopher R. Hoyle, Andreas Kürten, Aleksandr Kvashnin, Katrianne Lehtipalo, Naser Mahfouz, Vladimir Makhmutov, Roy L. Mauldin III, Ugo Molteni, Lauriane L. J. Quéléver, Matti Rissanen, Siegfried Schobesberger, Mario Simon, Andrea C. Wagner, Mingyi Wang, Chao Yan, Penglin Ye, Ilona Riipinen, Hamish Gordon, Joachim Curtius, Armin Hansel, Imad El Haddad, Markku Kulmala, Douglas R. Worsnop, Rainer Volkamer, Paul M. Winkler, Jasper Kirkby, and Richard Flagan
EGUsphere, https://doi.org/10.5194/egusphere-2025-2412, https://doi.org/10.5194/egusphere-2025-2412, 2025
This preprint is open for discussion and under review for Atmospheric Measurement Techniques (AMT).
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We describe accurate measurement of particle formation and growth in the CERN CLOUD chamber, using a suite of gas- and particle-phase instruments. The interconnected measurements establish high accuracy in key particle properties and critically important gas-phase sulfuric acid. This is a template for accurate calibration of similar experiments and thus accurate determination of aerosol nucleation and growth rates, which are an important source of uncertainty in climate science.
Giannis Ioannidis, Nikoletta Bouloti, Paul Tremper, Chaofan Li, Christos Boikos, Nikolaos Rapkos, Till Riedel, Miikka Dal Maso, and Leonidas Ntziachristos
EGUsphere, https://doi.org/10.5194/egusphere-2025-193, https://doi.org/10.5194/egusphere-2025-193, 2025
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This study introduces SOMA (Secondary Organic Module for Aerosol) to model SOA formation in urban environments, using VOC oxidation inputs from GECKO-A. Based on SOA formation experiments, SOMA incorporates correction factors for calibration purposes. A CFD model simulates toluene dispersion in Augsburg, and it’s linked to SOMA to show that background SOA contributes 21–53 % of total mass, fading after 7 hours, providing better understanding of SOA formation dynamics.
Federica Bortolussi, Hilda Sandström, Fariba Partovi, Joona Mikkilä, Patrick Rinke, and Matti Rissanen
Atmos. Chem. Phys., 25, 685–704, https://doi.org/10.5194/acp-25-685-2025, https://doi.org/10.5194/acp-25-685-2025, 2025
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Chemical ionization mass spectrometry (CIMS) is widely used in atmospheric chemistry studies. We still have a limited understanding of the complex functioning of the instrument; therefore, we applied machine learning to provide insights from CIMS analyses. We were able to predict both detection and signal intensity with a fair error, and we found out the most important structural fragments for negative ionization schemes (NH and OH) and positive ones (nitrogen-containing groups).
Henning Finkenzeller, Jyri Mikkilä, Cecilia Righi, Paxton Juuti, Mikko Sipilä, Matti Rissanen, Douglas Worsnop, Aleksei Shcherbinin, Nina Sarnela, and Juha Kangasluoma
Atmos. Meas. Tech., 17, 5989–6001, https://doi.org/10.5194/amt-17-5989-2024, https://doi.org/10.5194/amt-17-5989-2024, 2024
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Chemical ionisation mass spectrometry is used in the atmospheric sciences to measure trace gas concentrations. Neutral gases require charging in inlets before the mass-to-charge ratio of the resulting ions can be analysed. This study uses multiphysics modelling to investigate how the MION2 and Eisele type inlets work and shows the effect of tuning parameters and their current limitations. The findings are helpful for inlet users and are expected to aid in developing improved inlets.
Teemu Lepistö, Henna Lintusaari, Laura Salo, Ville Silvonen, Luis M. F. Barreira, Jussi Hoivala, Lassi Markkula, Jarkko V. Niemi, Jakub Ondracek, Kimmo Teinilä, Hanna E. Manninen, Sanna Saarikoski, Hilkka Timonen, Miikka Dal Maso, and Topi Rönkkö
Aerosol Research, 2, 271–289, https://doi.org/10.5194/ar-2-271-2024, https://doi.org/10.5194/ar-2-271-2024, 2024
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The performances of different particle lung-deposited surface area (LDSAal) measurement methods (Partector, ELPI+, SMPS/DMPS) were compared in ambient conditions. As LDSAal is a health-relevant metric and rather easy to utilise in air quality monitoring, it is crucial to know how the different methods agree, as there are clear differences in their operation. In all, a comparison of different methods can be complicated; still, the methods agree rather well in terms of local pollution (< 400 nm).
Alex Rowell, James Brean, David C. S. Beddows, Zongbo Shi, Avinash Kumar, Matti Rissanen, Miikka Dal Maso, Peter Mettke, Kay Weinhold, Maik Merkel, and Roy M. Harrison
Atmos. Chem. Phys., 24, 10349–10361, https://doi.org/10.5194/acp-24-10349-2024, https://doi.org/10.5194/acp-24-10349-2024, 2024
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Ions enhance the formation and growth rates of new particles, affecting the Earth's radiation budget. Despite these effects, there is little published data exploring the sources of ions in the urban environment and their role in new particle formation (NPF). Here we show that natural ion sources dominate in urban environments, while traffic is a secondary source. Ions contribute up to 12.7 % of the formation rate of particles, indicating that they are important for forming urban PM.
Stéphanie Alage, Vincent Michoud, Sergio Harb, Bénédicte Picquet-Varrault, Manuela Cirtog, Avinash Kumar, Matti Rissanen, and Christopher Cantrell
Atmos. Meas. Tech., 17, 4709–4724, https://doi.org/10.5194/amt-17-4709-2024, https://doi.org/10.5194/amt-17-4709-2024, 2024
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Calibration exercises are essential for determining the accuracy of instruments. We performed calibrations on a NO3¯ ToFCIMS instrument to determine its sensitivity and linearity for detecting various organic compounds. Our findings revealed significant variability, over several orders of magnitude, in the calibration factors obtained. The results suggest that relying on a single calibration factor from H2SO4 for the quantification of all compounds detected by this technique is not appropriate.
Pauli Simonen, Miikka Dal Maso, Pinja Prauda, Anniina Hoilijoki, Anette Karppinen, Pekka Matilainen, Panu Karjalainen, and Jorma Keskinen
Atmos. Meas. Tech., 17, 3219–3236, https://doi.org/10.5194/amt-17-3219-2024, https://doi.org/10.5194/amt-17-3219-2024, 2024
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Secondary aerosol is formed in the atmosphere from gaseous emissions. Oxidation flow reactors used in secondary aerosol research do not immediately respond to changes in the inlet concentration of gases because of their broad transfer functions. This may result in incorrect secondary aerosol production factors determined for vehicles. We studied the extent of possible errors and found that oxidation flow reactors with faster responses result in smaller errors.
Romain Salignat, Matti Rissanen, Siddharth Iyer, Jean-Luc Baray, Pierre Tulet, Jean-Marc Metzger, Jérôme Brioude, Karine Sellegri, and Clémence Rose
Atmos. Chem. Phys., 24, 3785–3812, https://doi.org/10.5194/acp-24-3785-2024, https://doi.org/10.5194/acp-24-3785-2024, 2024
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Using mass spectrometry data collected at the Maïdo Observatory (2160 m a.s.l., Réunion), we provide the first detailed analysis of molecular cluster chemical composition specifically in the marine free troposphere. The abundance of the identified species is related both to in situ meteorological parameters and air mass history, which also provide insight into their origin. Our work makes an important contribution to documenting the chemistry and physics of the marine free troposphere.
Magdalena Okuljar, Olga Garmash, Miska Olin, Joni Kalliokoski, Hilkka Timonen, Jarkko V. Niemi, Pauli Paasonen, Jenni Kontkanen, Yanjun Zhang, Heidi Hellén, Heino Kuuluvainen, Minna Aurela, Hanna E. Manninen, Mikko Sipilä, Topi Rönkkö, Tuukka Petäjä, Markku Kulmala, Miikka Dal Maso, and Mikael Ehn
Atmos. Chem. Phys., 23, 12965–12983, https://doi.org/10.5194/acp-23-12965-2023, https://doi.org/10.5194/acp-23-12965-2023, 2023
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Highly oxygenated organic molecules (HOMs) form secondary organic aerosol that affects air quality and health. In this study, we demonstrate that in a moderately polluted city with abundant vegetation, the composition of HOMs is largely controlled by the effect of NOx on the biogenic volatile organic compound oxidation. Comparing the results from two nearby stations, we show that HOM composition and formation pathways can change considerably within small distances in urban environments.
Xu-Cheng He, Jiali Shen, Siddharth Iyer, Paxton Juuti, Jiangyi Zhang, Mrisha Koirala, Mikko M. Kytökari, Douglas R. Worsnop, Matti Rissanen, Markku Kulmala, Norbert M. Maier, Jyri Mikkilä, Mikko Sipilä, and Juha Kangasluoma
Atmos. Meas. Tech., 16, 4461–4487, https://doi.org/10.5194/amt-16-4461-2023, https://doi.org/10.5194/amt-16-4461-2023, 2023
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In this study, the upgraded multi-scheme chemical ionisation inlet 2 is presented. Sulfuric acid, hypoiodous acid, iodine, sulfur dioxide, and hydroperoxyl radicals are calibrated, and the improved ion optics allow us to detect sulfuric acid and iodine-containing molecules at as low as a few parts per quadrillion by volume. Additionally, we confirm the reliable detection of iodic acid using both the nitrate and bromide chemical ionisation methods under atmospherically relevant conditions.
Shawon Barua, Siddharth Iyer, Avinash Kumar, Prasenjit Seal, and Matti Rissanen
Atmos. Chem. Phys., 23, 10517–10532, https://doi.org/10.5194/acp-23-10517-2023, https://doi.org/10.5194/acp-23-10517-2023, 2023
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This work illustrates how a common volatile hydrocarbon, hexanal, has the potential to undergo atmospheric autoxidation that leads to prompt formation of condensable material that subsequently contributes to aerosol formation, deteriorating the air quality of urban atmospheres. We used the combined state-of-the-art quantum chemical modeling and experimental flow reactor experiments under atmospheric conditions to resolve the autoxidation mechanism of hexanal initiated by a common oxidant.
Lukas Pichelstorfer, Pontus Roldin, Matti Rissanen, Noora Hyttinen, Olga Garmash, Carlton Xavier, Putian Zhou, Petri Clusius, Benjamin Foreback, Thomas Golin Almeida, Chenjuan Deng, Metin Baykara, Theo Kurten, and Michael Boy
EGUsphere, https://doi.org/10.5194/egusphere-2023-1415, https://doi.org/10.5194/egusphere-2023-1415, 2023
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Secondary organic aerosols (SOA) form effectively from gaseous precursors via a process called autoxidation. While key chemical reaction types seem to be known, no general description of autoxidation chemistry exists. In the present work, we present a method to create autoxidation chemistry schemes for any atmospherically relevant hydrocarbon. We exemplarily investigate benzene and its potential to form aerosols. We found that autoxidation, under some conditions, can dominate the SOA formation.
Melissa Meder, Otso Peräkylä, Jonathan G. Varelas, Jingyi Luo, Runlong Cai, Yanjun Zhang, Theo Kurtén, Matthieu Riva, Matti Rissanen, Franz M. Geiger, Regan J. Thomson, and Mikael Ehn
Atmos. Chem. Phys., 23, 4373–4390, https://doi.org/10.5194/acp-23-4373-2023, https://doi.org/10.5194/acp-23-4373-2023, 2023
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We discuss and show the viability of a method where multiple isotopically labelled precursors are used for probing the formation pathways of highly oxygenated organic molecules (HOMs) from the oxidation of the monoterpene a-pinene. HOMs are very important for secondary organic aerosol (SOA) formation in forested regions, and monoterpenes are the single largest source of SOA globally. The fast reactions forming HOMs have thus far remained elusive despite considerable efforts over the last decade.
Miska Olin, Magdalena Okuljar, Matti P. Rissanen, Joni Kalliokoski, Jiali Shen, Lubna Dada, Markus Lampimäki, Yusheng Wu, Annalea Lohila, Jonathan Duplissy, Mikko Sipilä, Tuukka Petäjä, Markku Kulmala, and Miikka Dal Maso
Atmos. Chem. Phys., 22, 8097–8115, https://doi.org/10.5194/acp-22-8097-2022, https://doi.org/10.5194/acp-22-8097-2022, 2022
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Atmospheric new particle formation is an important source of the total particle number concentration in the atmosphere. Several parameters for predicting new particle formation events have been suggested before, but the results have been inconclusive. This study proposes an another predicting parameter, related to a specific type of highly oxidized organic molecules, especially for similar locations to the measurement site in this study, which was a coastal agricultural site in Finland.
Matthias Karl, Liisa Pirjola, Tiia Grönholm, Mona Kurppa, Srinivasan Anand, Xiaole Zhang, Andreas Held, Rolf Sander, Miikka Dal Maso, David Topping, Shuai Jiang, Leena Kangas, and Jaakko Kukkonen
Geosci. Model Dev., 15, 3969–4026, https://doi.org/10.5194/gmd-15-3969-2022, https://doi.org/10.5194/gmd-15-3969-2022, 2022
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The community aerosol dynamics model MAFOR includes several advanced features: coupling with an up-to-date chemistry mechanism for volatile organic compounds, a revised Brownian coagulation kernel that takes into account the fractal geometry of soot particles, a multitude of nucleation parameterizations, size-resolved partitioning of semi-volatile inorganics, and a hybrid method for the formation of secondary organic aerosols within the framework of condensation and evaporation.
Miska Olin, David Patoulias, Heino Kuuluvainen, Jarkko V. Niemi, Topi Rönkkö, Spyros N. Pandis, Ilona Riipinen, and Miikka Dal Maso
Atmos. Chem. Phys., 22, 1131–1148, https://doi.org/10.5194/acp-22-1131-2022, https://doi.org/10.5194/acp-22-1131-2022, 2022
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An emission factor particle size distribution was determined from the measurements at an urban traffic site. It was used in updating a pre-existing emission inventory, and regional modeling was performed after the update. Emission inventories typically underestimate nanoparticle emissions due to challenges in determining them with high certainty. This update reveals that the simulated aerosol levels have previously been underestimated especially for urban areas and for sub-50 nm particles.
Dalrin Ampritta Amaladhasan, Claudia Heyn, Christopher R. Hoyle, Imad El Haddad, Miriam Elser, Simone M. Pieber, Jay G. Slowik, Antonio Amorim, Jonathan Duplissy, Sebastian Ehrhart, Vladimir Makhmutov, Ugo Molteni, Matti Rissanen, Yuri Stozhkov, Robert Wagner, Armin Hansel, Jasper Kirkby, Neil M. Donahue, Rainer Volkamer, Urs Baltensperger, Martin Gysel-Beer, and Andreas Zuend
Atmos. Chem. Phys., 22, 215–244, https://doi.org/10.5194/acp-22-215-2022, https://doi.org/10.5194/acp-22-215-2022, 2022
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We use a combination of models for gas-phase chemical reactions and equilibrium gas–particle partitioning of isoprene-derived secondary organic aerosols (SOAs) informed by dark ozonolysis experiments conducted in the CLOUD chamber. Our predictions cover high to low relative humidities (RHs) and quantify how SOA mass yields are enhanced at high RH as well as the impact of inorganic seeds of distinct hygroscopicities and acidities on the coupled partitioning of water and semi-volatile organics.
Mao Xiao, Christopher R. Hoyle, Lubna Dada, Dominik Stolzenburg, Andreas Kürten, Mingyi Wang, Houssni Lamkaddam, Olga Garmash, Bernhard Mentler, Ugo Molteni, Andrea Baccarini, Mario Simon, Xu-Cheng He, Katrianne Lehtipalo, Lauri R. Ahonen, Rima Baalbaki, Paulus S. Bauer, Lisa Beck, David Bell, Federico Bianchi, Sophia Brilke, Dexian Chen, Randall Chiu, António Dias, Jonathan Duplissy, Henning Finkenzeller, Hamish Gordon, Victoria Hofbauer, Changhyuk Kim, Theodore K. Koenig, Janne Lampilahti, Chuan Ping Lee, Zijun Li, Huajun Mai, Vladimir Makhmutov, Hanna E. Manninen, Ruby Marten, Serge Mathot, Roy L. Mauldin, Wei Nie, Antti Onnela, Eva Partoll, Tuukka Petäjä, Joschka Pfeifer, Veronika Pospisilova, Lauriane L. J. Quéléver, Matti Rissanen, Siegfried Schobesberger, Simone Schuchmann, Yuri Stozhkov, Christian Tauber, Yee Jun Tham, António Tomé, Miguel Vazquez-Pufleau, Andrea C. Wagner, Robert Wagner, Yonghong Wang, Lena Weitz, Daniela Wimmer, Yusheng Wu, Chao Yan, Penglin Ye, Qing Ye, Qiaozhi Zha, Xueqin Zhou, Antonio Amorim, Ken Carslaw, Joachim Curtius, Armin Hansel, Rainer Volkamer, Paul M. Winkler, Richard C. Flagan, Markku Kulmala, Douglas R. Worsnop, Jasper Kirkby, Neil M. Donahue, Urs Baltensperger, Imad El Haddad, and Josef Dommen
Atmos. Chem. Phys., 21, 14275–14291, https://doi.org/10.5194/acp-21-14275-2021, https://doi.org/10.5194/acp-21-14275-2021, 2021
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Experiments at CLOUD show that in polluted environments new particle formation (NPF) is largely driven by the formation of sulfuric acid–base clusters, stabilized by amines, high ammonia concentrations or lower temperatures. While oxidation products of aromatics can nucleate, they play a minor role in urban NPF. Our experiments span 4 orders of magnitude variation of observed NPF rates in ambient conditions. We provide a framework based on NPF and growth rates to interpret ambient observations.
Magdalena Okuljar, Heino Kuuluvainen, Jenni Kontkanen, Olga Garmash, Miska Olin, Jarkko V. Niemi, Hilkka Timonen, Juha Kangasluoma, Yee Jun Tham, Rima Baalbaki, Mikko Sipilä, Laura Salo, Henna Lintusaari, Harri Portin, Kimmo Teinilä, Minna Aurela, Miikka Dal Maso, Topi Rönkkö, Tuukka Petäjä, and Pauli Paasonen
Atmos. Chem. Phys., 21, 9931–9953, https://doi.org/10.5194/acp-21-9931-2021, https://doi.org/10.5194/acp-21-9931-2021, 2021
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To estimate the relative contribution of different sources to the particle population in an urban environment, we conducted simultaneous measurements at a street canyon and an urban background station in Helsinki. We investigated the contribution of traffic and new particle formation to particles with a diameter between 1 and 800 nm. We found that during spring traffic does not dominate the particles smaller than 3 nm at either of the stations.
Mingyi Wang, Xu-Cheng He, Henning Finkenzeller, Siddharth Iyer, Dexian Chen, Jiali Shen, Mario Simon, Victoria Hofbauer, Jasper Kirkby, Joachim Curtius, Norbert Maier, Theo Kurtén, Douglas R. Worsnop, Markku Kulmala, Matti Rissanen, Rainer Volkamer, Yee Jun Tham, Neil M. Donahue, and Mikko Sipilä
Atmos. Meas. Tech., 14, 4187–4202, https://doi.org/10.5194/amt-14-4187-2021, https://doi.org/10.5194/amt-14-4187-2021, 2021
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Atmospheric iodine species are often short-lived with low abundance and have thus been challenging to measure. We show that the bromide chemical ionization mass spectrometry, compatible with both the atmospheric pressure and reduced pressure interfaces, can simultaneously detect various gas-phase iodine species. Combining calibration experiments and quantum chemical calculations, we quantify detection sensitivities to HOI, HIO3, I2, and H2SO4, giving detection limits down to < 106 molec. cm-3.
Meri Räty, Otso Peräkylä, Matthieu Riva, Lauriane Quéléver, Olga Garmash, Matti Rissanen, and Mikael Ehn
Atmos. Chem. Phys., 21, 7357–7372, https://doi.org/10.5194/acp-21-7357-2021, https://doi.org/10.5194/acp-21-7357-2021, 2021
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Cyclohexene resembles certain relatively complex compounds in the atmosphere that through oxidation produce vapours that take part in aerosol formation. We studied the highly oxygenated organic molecules (HOMs) formed in cyclohexene ozonolysis, the relationship between their chemical composition and their tendency to condense onto seed aerosol, as well as the effect of NOx pollutants on their signals. Two existing models were also tested for their ability to predict the volatility of the HOMs.
Clémence Rose, Matti P. Rissanen, Siddharth Iyer, Jonathan Duplissy, Chao Yan, John B. Nowak, Aurélie Colomb, Régis Dupuy, Xu-Cheng He, Janne Lampilahti, Yee Jun Tham, Daniela Wimmer, Jean-Marc Metzger, Pierre Tulet, Jérôme Brioude, Céline Planche, Markku Kulmala, and Karine Sellegri
Atmos. Chem. Phys., 21, 4541–4560, https://doi.org/10.5194/acp-21-4541-2021, https://doi.org/10.5194/acp-21-4541-2021, 2021
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Sulfuric acid (H2SO4) is commonly accepted as a key precursor for atmospheric new particle formation. However, direct measurements of [H2SO4] remain challenging, motivating the development of proxies. Using data collected in two different volcanic plumes, we show, under these specific conditions, the good performance of a proxy from the literature and also highlight the benefit of the newly developed proxies for the prediction of the highest [H2SO4] values.
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Short summary
We developed a computer program that can read chemical formulas and identify key features in thousands of organic compounds. This helps scientists estimate how easily these compounds evaporate, which is important for understanding air pollution and climate. We tested the program using real-world data and found it to be highly accurate. Our work makes it faster and easier to study the behavior of many complex chemicals in the atmosphere.
We developed a computer program that can read chemical formulas and identify key features in...
