Articles | Volume 17, issue 6
https://doi.org/10.5194/gmd-17-2419-2024
© Author(s) 2024. 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-17-2419-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
MEXPLORER 1.0.0 – a mechanism explorer for analysis and visualization of chemical reaction pathways based on graph theory
Air Chemistry Department, Max Planck Institute of Chemistry, P.O. Box 3060, 55020 Mainz, Germany
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Raphael Dreger, Timo Kirfel, Andrea Pozzer, Simon Rosanka, Rolf Sander, and Domenico Taraborrelli
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Model simulations are essential for understanding the interactions between atmospheric composition and weather. However, models including chemistry are very slow. Hence, any computation speedup of such models is important for understanding the role of atmospheric chemistry within the Earth system. In this study we analyzed and optimized the time step for chemistry calculations. Our results show that atmospheric models could be run notably faster without any loss in accuracy.
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Measurements and modelling of reactive nitrogen gases observed in a suburban temperate forest in Rambouillet, France, circa 50 km southwest of Paris in 2022 indicate that the biosphere rapidly scavenges organic nitrates of mixed biogenic and anthropogenic origin, resulting in short lifetimes for, for example, alkyl nitrates and peroxy nitrates.
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The chemistry scheme of the atmospheric box model CAABA/MECCA is expanded to achieve an improved aerosol formation from emitted organic compounds. In addition to newly added reactions, temperature-dependent partitioning of all new species between the gas and aqueous phases is estimated and included in the pre-existing scheme. Sensitivity runs show an overestimation of key compounds from isoprene, which can be explained by a lack of aqueous-phase degradation reactions and box model limitations.
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The capabilities of the Modular Earth Submodel System (MESSy) are extended to account for non-equilibrium aqueous-phase chemistry in the representation of deliquescent aerosols. When applying the new development in a global simulation, we find that MESSy's bias in modelling routinely observed reduced inorganic aerosol mass concentrations, especially in the United States. Furthermore, the representation of fine-aerosol pH is particularly improved in the marine boundary layer.
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The study presents the implementation of comprehensive multiphase chlorine chemistry in the box model CAABA/MECCA. Simulations for contrasting urban environments of Asia and Europe highlight the significant impacts of chlorine on atmospheric oxidation capacity and composition. Chemical processes governing the production and loss of chlorine-containing species has been discussed. The updated chemical mechanism will be useful to interpret field measurements and for future air quality studies.
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According to Henry's law, the equilibrium ratio between the abundances in the gas phase and in the aqueous phase is constant for a dilute solution. Henry’s law constants of trace gases of potential importance in environmental chemistry have been collected and converted into a uniform format. The compilation contains 46 434 values of Henry's law constants for 10 173 species, collected from 995 references. It is also available on the internet at https://www.henrys-law.org.
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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.
Andrea Pozzer, Simon F. Reifenberg, Vinod Kumar, Bruno Franco, Matthias Kohl, Domenico Taraborrelli, Sergey Gromov, Sebastian Ehrhart, Patrick Jöckel, Rolf Sander, Veronica Fall, Simon Rosanka, Vlassis Karydis, Dimitris Akritidis, Tamara Emmerichs, Monica Crippa, Diego Guizzardi, Johannes W. Kaiser, Lieven Clarisse, Astrid Kiendler-Scharr, Holger Tost, and Alexandra Tsimpidi
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A newly developed setup of the chemistry general circulation model EMAC (ECHAM5/MESSy for Atmospheric Chemistry) is evaluated here. A comprehensive organic degradation mechanism is used and coupled with a volatility base model.
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Philipp G. Eger, Luc Vereecken, Rolf Sander, Jan Schuladen, Nicolas Sobanski, Horst Fischer, Einar Karu, Jonathan Williams, Ville Vakkari, Tuukka Petäjä, Jos Lelieveld, Andrea Pozzer, and John N. Crowley
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We determine the impact of pyruvic acid photolysis on the formation of acetaldehyde and peroxy radicals during summer and autumn in the Finnish boreal forest using a data-constrained box model. Our results are dependent on the chosen scenario in which the overall quantum yield and the photolysis products are varied. We highlight that pyruvic acid photolysis can be an important contributor to acetaldehyde and peroxy radical formation in remote, forested regions.
Simon Rosanka, Rolf Sander, Andreas Wahner, and Domenico Taraborrelli
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The Jülich Aqueous-phase Mechanism of Organic Chemistry (JAMOC) is developed and implemented into the Module Efficiently Calculating the Chemistry of the Atmosphere (MECCA). JAMOC is an explicit in-cloud oxidation scheme for oxygenated volatile organic compounds (OVOCs), which is suitable for global model applications. Within a box-model study, we show that JAMOC yields reduced gas-phase concentrations of most OVOCs and oxidants, except for nitrogen oxides.
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In-cloud destruction of ozone depends on hydroperoxyl radicals in cloud droplets, where they are produced by oxygenated volatile organic compound (OVOC) oxygenation. Only rudimentary representations of these processes, if any, are currently available in global atmospheric models. By using a comprehensive atmospheric model that includes a complex in-cloud OVOC oxidation scheme, we show that atmospheric oxidants are reduced and models ignoring this process will underpredict clouds as ozone sinks.
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Atmospheric pollutants from anthropogenic activities and biomass burning are usually regarded as ozone precursors. Monocyclic aromatics are no exception. Calculations with a comprehensive atmospheric model are consistent with this view but only for air masses close to pollution source regions. However, the same model predicts that aromatics, when transported to remote areas, may effectively destroy ozone. This loss of tropospheric ozone rivals the one attributed to bromine.
Raphael Dreger, Timo Kirfel, Andrea Pozzer, Simon Rosanka, Rolf Sander, and Domenico Taraborrelli
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Short summary
Short summary
Model simulations are essential for understanding the interactions between atmospheric composition and weather. However, models including chemistry are very slow. Hence, any computation speedup of such models is important for understanding the role of atmospheric chemistry within the Earth system. In this study we analyzed and optimized the time step for chemistry calculations. Our results show that atmospheric models could be run notably faster without any loss in accuracy.
Simone T. Andersen, Rolf Sander, Patrick Dewald, Laura Wüst, Tobias Seubert, Gunther N. T. E. Türk, Jan Schuladen, Max R. McGillen, Chaoyang Xue, Abdelwahid Mellouki, Alexandre Kukui, Vincent Michoud, Manuela Cirtog, Mathieu Cazaunau, Astrid Bauville, Hichem Bouzidi, Paola Formenti, Cyrielle Denjean, Jean-Claude Etienne, Olivier Garrouste, Christopher Cantrell, Jos Lelieveld, and John N. Crowley
Atmos. Chem. Phys., 25, 5893–5909, https://doi.org/10.5194/acp-25-5893-2025, https://doi.org/10.5194/acp-25-5893-2025, 2025
Short summary
Short summary
Measurements and modelling of reactive nitrogen gases observed in a suburban temperate forest in Rambouillet, France, circa 50 km southwest of Paris in 2022 indicate that the biosphere rapidly scavenges organic nitrates of mixed biogenic and anthropogenic origin, resulting in short lifetimes for, for example, alkyl nitrates and peroxy nitrates.
Felix Wieser, Rolf Sander, Changmin Cho, Hendrik Fuchs, Thorsten Hohaus, Anna Novelli, Ralf Tillmann, and Domenico Taraborrelli
Geosci. Model Dev., 17, 4311–4330, https://doi.org/10.5194/gmd-17-4311-2024, https://doi.org/10.5194/gmd-17-4311-2024, 2024
Short summary
Short summary
The chemistry scheme of the atmospheric box model CAABA/MECCA is expanded to achieve an improved aerosol formation from emitted organic compounds. In addition to newly added reactions, temperature-dependent partitioning of all new species between the gas and aqueous phases is estimated and included in the pre-existing scheme. Sensitivity runs show an overestimation of key compounds from isoprene, which can be explained by a lack of aqueous-phase degradation reactions and box model limitations.
Simon Rosanka, Holger Tost, Rolf Sander, Patrick Jöckel, Astrid Kerkweg, and Domenico Taraborrelli
Geosci. Model Dev., 17, 2597–2615, https://doi.org/10.5194/gmd-17-2597-2024, https://doi.org/10.5194/gmd-17-2597-2024, 2024
Short summary
Short summary
The capabilities of the Modular Earth Submodel System (MESSy) are extended to account for non-equilibrium aqueous-phase chemistry in the representation of deliquescent aerosols. When applying the new development in a global simulation, we find that MESSy's bias in modelling routinely observed reduced inorganic aerosol mass concentrations, especially in the United States. Furthermore, the representation of fine-aerosol pH is particularly improved in the marine boundary layer.
Meghna Soni, Rolf Sander, Lokesh K. Sahu, Domenico Taraborrelli, Pengfei Liu, Ankit Patel, Imran A. Girach, Andrea Pozzer, Sachin S. Gunthe, and Narendra Ojha
Atmos. Chem. Phys., 23, 15165–15180, https://doi.org/10.5194/acp-23-15165-2023, https://doi.org/10.5194/acp-23-15165-2023, 2023
Short summary
Short summary
The study presents the implementation of comprehensive multiphase chlorine chemistry in the box model CAABA/MECCA. Simulations for contrasting urban environments of Asia and Europe highlight the significant impacts of chlorine on atmospheric oxidation capacity and composition. Chemical processes governing the production and loss of chlorine-containing species has been discussed. The updated chemical mechanism will be useful to interpret field measurements and for future air quality studies.
Rolf Sander
Atmos. Chem. Phys., 23, 10901–12440, https://doi.org/10.5194/acp-23-10901-2023, https://doi.org/10.5194/acp-23-10901-2023, 2023
Short summary
Short summary
According to Henry's law, the equilibrium ratio between the abundances in the gas phase and in the aqueous phase is constant for a dilute solution. Henry’s law constants of trace gases of potential importance in environmental chemistry have been collected and converted into a uniform format. The compilation contains 46 434 values of Henry's law constants for 10 173 species, collected from 995 references. It is also available on the internet at https://www.henrys-law.org.
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
Short summary
Short summary
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.
Andrea Pozzer, Simon F. Reifenberg, Vinod Kumar, Bruno Franco, Matthias Kohl, Domenico Taraborrelli, Sergey Gromov, Sebastian Ehrhart, Patrick Jöckel, Rolf Sander, Veronica Fall, Simon Rosanka, Vlassis Karydis, Dimitris Akritidis, Tamara Emmerichs, Monica Crippa, Diego Guizzardi, Johannes W. Kaiser, Lieven Clarisse, Astrid Kiendler-Scharr, Holger Tost, and Alexandra Tsimpidi
Geosci. Model Dev., 15, 2673–2710, https://doi.org/10.5194/gmd-15-2673-2022, https://doi.org/10.5194/gmd-15-2673-2022, 2022
Short summary
Short summary
A newly developed setup of the chemistry general circulation model EMAC (ECHAM5/MESSy for Atmospheric Chemistry) is evaluated here. A comprehensive organic degradation mechanism is used and coupled with a volatility base model.
The results show that the model reproduces most of the tracers and aerosols satisfactorily but shows discrepancies for oxygenated organic gases. It is also shown that this model configuration can be used for further research in atmospheric chemistry.
Philipp G. Eger, Luc Vereecken, Rolf Sander, Jan Schuladen, Nicolas Sobanski, Horst Fischer, Einar Karu, Jonathan Williams, Ville Vakkari, Tuukka Petäjä, Jos Lelieveld, Andrea Pozzer, and John N. Crowley
Atmos. Chem. Phys., 21, 14333–14349, https://doi.org/10.5194/acp-21-14333-2021, https://doi.org/10.5194/acp-21-14333-2021, 2021
Short summary
Short summary
We determine the impact of pyruvic acid photolysis on the formation of acetaldehyde and peroxy radicals during summer and autumn in the Finnish boreal forest using a data-constrained box model. Our results are dependent on the chosen scenario in which the overall quantum yield and the photolysis products are varied. We highlight that pyruvic acid photolysis can be an important contributor to acetaldehyde and peroxy radical formation in remote, forested regions.
Simon Rosanka, Rolf Sander, Andreas Wahner, and Domenico Taraborrelli
Geosci. Model Dev., 14, 4103–4115, https://doi.org/10.5194/gmd-14-4103-2021, https://doi.org/10.5194/gmd-14-4103-2021, 2021
Short summary
Short summary
The Jülich Aqueous-phase Mechanism of Organic Chemistry (JAMOC) is developed and implemented into the Module Efficiently Calculating the Chemistry of the Atmosphere (MECCA). JAMOC is an explicit in-cloud oxidation scheme for oxygenated volatile organic compounds (OVOCs), which is suitable for global model applications. Within a box-model study, we show that JAMOC yields reduced gas-phase concentrations of most OVOCs and oxidants, except for nitrogen oxides.
Simon Rosanka, Rolf Sander, Bruno Franco, Catherine Wespes, Andreas Wahner, and Domenico Taraborrelli
Atmos. Chem. Phys., 21, 9909–9930, https://doi.org/10.5194/acp-21-9909-2021, https://doi.org/10.5194/acp-21-9909-2021, 2021
Short summary
Short summary
In-cloud destruction of ozone depends on hydroperoxyl radicals in cloud droplets, where they are produced by oxygenated volatile organic compound (OVOC) oxygenation. Only rudimentary representations of these processes, if any, are currently available in global atmospheric models. By using a comprehensive atmospheric model that includes a complex in-cloud OVOC oxidation scheme, we show that atmospheric oxidants are reduced and models ignoring this process will underpredict clouds as ozone sinks.
Julian Rüdiger, Alexandra Gutmann, Nicole Bobrowski, Marcello Liotta, J. Maarten de Moor, Rolf Sander, Florian Dinger, Jan-Lukas Tirpitz, Martha Ibarra, Armando Saballos, María Martínez, Elvis Mendoza, Arnoldo Ferrufino, John Stix, Juan Valdés, Jonathan M. Castro, and Thorsten Hoffmann
Atmos. Chem. Phys., 21, 3371–3393, https://doi.org/10.5194/acp-21-3371-2021, https://doi.org/10.5194/acp-21-3371-2021, 2021
Short summary
Short summary
We present an innovative approach to study halogen chemistry in the plume of Masaya volcano in Nicaragua. An unique data set was collected using multiple techniques, including drones. These data enabled us to determine the fraction of activation of the respective halogens at various plume ages, where in-mixing of ambient air causes chemical reactions. An atmospheric chemistry box model was employed to further examine the field results and help our understanding of volcanic plume chemistry.
Domenico Taraborrelli, David Cabrera-Perez, Sara Bacer, Sergey Gromov, Jos Lelieveld, Rolf Sander, and Andrea Pozzer
Atmos. Chem. Phys., 21, 2615–2636, https://doi.org/10.5194/acp-21-2615-2021, https://doi.org/10.5194/acp-21-2615-2021, 2021
Short summary
Short summary
Atmospheric pollutants from anthropogenic activities and biomass burning are usually regarded as ozone precursors. Monocyclic aromatics are no exception. Calculations with a comprehensive atmospheric model are consistent with this view but only for air masses close to pollution source regions. However, the same model predicts that aromatics, when transported to remote areas, may effectively destroy ozone. This loss of tropospheric ozone rivals the one attributed to bromine.
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Short summary
The open-source software MEXPLORER 1.0.0 is presented here. The program can be used to analyze, reduce, and visualize complex chemical reaction mechanisms. The mathematics behind the tool is based on graph theory: chemical species are represented as vertices, and reactions as edges. MEXPLORER is a community model published under the GNU General Public License.
The open-source software MEXPLORER 1.0.0 is presented here. The program can be used to analyze,...