scholarly journals Oxidation of low-molecular-weight organic compounds in cloud droplets: development of the Jülich Aqueous-phase Mechanism of Organic Chemistry (JAMOC) in CAABA/MECCA (version 4.5.0)

2021 ◽  
Vol 14 (6) ◽  
pp. 4103-4115
Author(s):  
Simon Rosanka ◽  
Rolf Sander ◽  
Andreas Wahner ◽  
Domenico Taraborrelli

Abstract. The Jülich Aqueous-phase Mechanism of Organic Chemistry (JAMOC) is developed and implemented in the Module Efficiently Calculating the Chemistry of the Atmosphere (MECCA; version 4.5.0). JAMOC is an explicit in-cloud oxidation scheme for oxygenated volatile organic compounds (OVOCs), suitable for global model applications. It is based on a subset of the comprehensive Cloud Explicit Physico-chemical Scheme (CLEPS; version 1.0). The phase transfer of species containing up to 10 carbon atoms is included, and a selection of species containing up to 4 carbon atoms reacts in the aqueous phase. In addition, the following main advances are implemented: (1) simulating hydration and dehydration explicitly; (2) taking oligomerisation of formaldehyde, glyoxal, and methylglyoxal into account; (3) adding further photolysis reactions; and (4) considering gas-phase oxidation of new outgassed species. The implementation of JAMOC in MECCA makes a detailed in-cloud OVOC oxidation model readily available for box as well as for regional and global simulations that are affordable with modern supercomputing facilities. The new mechanism is tested inside the box model Chemistry As A Boxmodel Application (CAABA), yielding reduced gas-phase concentrations of most oxidants and OVOCs except for the nitrogen oxides.

2020 ◽  
Author(s):  
Simon Rosanka ◽  
Rolf Sander ◽  
Andreas Wahner ◽  
Domenico Taraborrelli

Abstract. The Jülich Aqueous-phase Mechanism of Organic Chemistry (JAMOC) is developed and implemented in the Module Efficiently Calculating the Chemistry of the Atmosphere (MECCA, version 4.5.0gmdd1). JAMOC is an explicit in-cloud oxidation scheme for oxygenated volatile organic compounds (OVOCs), suitable for global model applications. It is based on a subset of the comprehensive CLoud Explicit Physico-chemical Scheme (CLEPS, version 1.0). The phase transfer of species containing up to ten carbon atoms is included, and a selection of species containing up to four carbon atoms reacts in the aqueous-phase. In addition, the following main advances are implemented: (1) simulating hydration and dehydration explicitly, (2) taking oligomerisation of formaldehyde, glyoxal and methylglyoxal into account, (3) adding further photolysis reactions, and (4) considering gas-phase oxidation of new outgassed species. The implementation of JAMOC in MECCA makes a detailed in-cloud OVOC oxidation model readily available for box as well as for regional and global simulations that are affordable with modern supercomputing facilities. The new mechanism is tested inside the box-model Chemistry As A Boxmodel Application (CAABA), yielding reduced gas-phase concentrations of most oxidants and OVOCs except for the nitrogen oxides. 1 The name of this version indicates that it is used for the interactive discussion in GMDD. If necessary, bug fixes can still be made. We plan to release the final version CAABA/MECCA-4.5.0 together with the final paper in GMD.


2017 ◽  
Vol 10 (3) ◽  
pp. 1339-1362 ◽  
Author(s):  
Camille Mouchel-Vallon ◽  
Laurent Deguillaume ◽  
Anne Monod ◽  
Hélène Perroux ◽  
Clémence Rose ◽  
...  

Abstract. A new detailed aqueous phase mechanism named the Cloud Explicit Physico-chemical Scheme (CLEPS 1.0) is proposed to describe the oxidation of water soluble organic compounds resulting from isoprene oxidation. It is based on structure activity relationships (SARs) which provide global rate constants together with branching ratios for HO⋅ abstraction and addition on atmospheric organic compounds. The GROMHE SAR allows the evaluation of Henry's law constants for undocumented organic compounds. This new aqueous phase mechanism is coupled with the MCM v3.3.1 gas phase mechanism through a mass transfer scheme between gas phase and aqueous phase. The resulting multiphase mechanism has then been implemented in a model based on the Dynamically Simple Model for Atmospheric Chemical Complexity (DSMACC) using the Kinetic PreProcessor (KPP) that can serve to analyze data from cloud chamber experiments and field campaigns. The simulation of permanent cloud under low-NOx conditions describes the formation of oxidized monoacids and diacids in the aqueous phase as well as a significant influence on the gas phase chemistry and composition and shows that the aqueous phase reactivity leads to an efficient fragmentation and functionalization of organic compounds.


2021 ◽  
Author(s):  
Simon Rosanka ◽  
Rolf Sander ◽  
Bruno Franco ◽  
Catherine Wespes ◽  
Andreas Wahner ◽  
...  

<p>Large parts of the troposphere are affected by clouds, whose aqueous-phase chemistry differs significantly from gas-phase chemistry. Box-model studies have demonstrated that clouds influence the tropospheric oxidation capacity. However, most global atmospheric models do not represent this chemistry reasonably well and are largely limited to sulfur oxidation. Therefore, we have developed the Jülich Aqueous-phase Mechanism of Organic Chemistry (JAMOC), making a detailed in-cloud oxidation model of oxygenated volatile organic compounds (OVOCs) readily available for box as well as for regional and global simulations that are affordable with modern supercomputers. JAMOC includes the phase transfer of species containing up to ten carbon atoms, and the aqueous-phase reactions of a selection of species containing up to four carbon atoms, e.g., ethanol, acetaldehyde, glyoxal. The impact of in-cloud chemistry on tropospheric composition is assessed on a regional and global scale by performing a combination of box-model studies using the Chemistry As A Boxmodel Application (CAABA) and the global atmospheric model ECHAM/MESSy (EMAC). These models are capable to represent the described processes explicitly and integrate the corresponding ODE system with a Rosenbrock solver. </p><p>Overall, the explicit in-cloud oxidation leads to a reduction of predicted OVOCs levels. By comparing EMAC's prediction of methanol abundance to spaceborne retrievals from the Infrared Atmospheric Sounding Interferometer (IASI), a reduction in EMAC's overestimation is observed in the tropics. Further, the in-cloud OVOC oxidation shifts the hydroperoxyl radicals (HO<sub>2</sub>) production from the gas- to the aqueous-phase. As a result, the in-cloud destruction (scavenging) of ozone (O<sub>3</sub>) by the superoxide anion (O<sub>2</sub><sup>-</sup>) is enhanced and accompanied by a reduction in both sources and sinks of tropospheric O<sub>3</sub> in the gas phase. By considering only the in-cloud sulfur oxidation by O<sub>3</sub>, about 13 Tg a<sup>-1</sup> of O<sub>3</sub> are scavenged, which increases to 336 Tg a<sup>-1</sup> when JAMOC is used. With the full oxidation scheme, the highest O<sub>3</sub> reduction of 12 % is predicted in the upper troposphere/lower stratosphere (UTLS). Based on the IASI O<sub>3</sub> retrievals, it is demonstrated that these changes in the free troposphere significantly reduce the modelled tropospheric O<sub>3</sub> columns, which are known to be generally overestimated by global atmospheric models. Finally, the relevance of aqueous-phase oxidation of organics for ozone in hazy polluted regions will be presented.  </p>


2016 ◽  
Vol 16 (1) ◽  
pp. 277-292 ◽  
Author(s):  
W. Jud ◽  
L. Fischer ◽  
E. Canaval ◽  
G. Wohlfahrt ◽  
A. Tissier ◽  
...  

Abstract. Elevated tropospheric ozone concentrations are considered a toxic threat to plants, responsible for global crop losses with associated economic costs of several billion dollars per year. Plant injuries have been linked to the uptake of ozone through stomatal pores and oxidative damage of the internal leaf tissue. But a striking question remains: can surface reactions limit the stomatal uptake of ozone and therefore reduce its detrimental effects to plants?In this laboratory study we could show that semi-volatile organic compounds exuded by the glandular trichomes of different Nicotiana tabacum varieties are an efficient ozone sink at the plant surface. In our experiments, different diterpenoid compounds were responsible for a strongly variety-dependent ozone uptake of plants under dark conditions, when stomatal pores are almost closed. Surface reactions of ozone were accompanied by a prompt release of oxygenated volatile organic compounds, which could be linked to the corresponding precursor compounds: ozonolysis cis-abienol (C20H34O) – a diterpenoid with two exocyclic double bonds – caused emissions of formaldehyde (HCHO) and methyl vinyl ketone (C4H6O). The ring-structured cembratrien-diols (C20H34O2) with three endocyclic double bonds need at least two ozonolysis steps to form volatile carbonyls such as 4-oxopentanal (C5H8O2), which we could observe in the gas phase, too.Fluid dynamic calculations were used to model ozone distribution in the diffusion-limited leaf boundary layer under daylight conditions. In the case of an ozone-reactive leaf surface, ozone gradients in the vicinity of stomatal pores are changed in such a way that the ozone flux through the open stomata is strongly reduced.Our results show that unsaturated semi-volatile compounds at the plant surface should be considered as a source of oxygenated volatile organic compounds, impacting gas phase chemistry, as well as efficient ozone sink improving the ozone tolerance of plants.


2011 ◽  
Vol 11 (15) ◽  
pp. 7399-7415 ◽  
Author(s):  
D. Huang ◽  
X. Zhang ◽  
Z. M. Chen ◽  
Y. Zhao ◽  
X. L. Shen

Abstract. Aqueous phase chemical processes of organic compounds in the atmosphere have received increasing attention, partly due to their potential contribution to the formation of secondary organic aerosol (SOA). Here, we analyzed the aqueous OH-initiated oxidation of isoprene and its reaction products including carbonyl compounds and organic acids, regarding the acidity and temperature as in-cloudy conditions. We also performed a laboratory simulation to improve our understanding of the kinetics and mechanisms for the products of aqueous isoprene oxidation that are significant precursors of SOA; these included methacrolein (MACR), methyl vinyl ketone (MVK), methyl glyoxal (MG), and glyoxal (GL). We used a novel chemical titration method to monitor the concentration of isoprene in the aqueous phase. We used a box model to interpret the mechanistic differences between aqueous and gas phase OH radical-initiated isoprene oxidations. Our results were the first demonstration of the rate constant for the reaction between isoprene and OH radical in water, 1.2 ± 0.4) × 1010 M−1 s−1 at 283 K. Molar yields were determined based on consumed isoprene. Of note, the ratio of the yields of MVK (24.1 ± 0.8 %) to MACR (10.9 ± 1.1%) in the aqueous phase isoprene oxidation was approximately double that observed for the corresponding gas phase reaction. We hypothesized that this might be explained by a water-induced enhancement in the self-reaction of a hydroxy isoprene peroxyl radical (HOCH2C(CH3)(O2)CH = CH2) produced in the aqueous reaction. The observed yields for MG and GL were 11.4 ± 0.3 % and 3.8 ± 0.1 %, respectively. Model simulations indicated that several potential pathways may contribute to the formation of MG and GL. Finally, oxalic acid increased steadily throughout the course of the study, even after isoprene was consumed completely. The observed yield of oxalic acid was 26.2 ± 0.8 % at 6 h. The observed carbon balance accounted for ~50 % of the consumed isoprene. The presence of high-molecular-weight compounds may have accounted for a large portion of the missing carbons, but they were not quantified in this study. In summary, our work has provided experimental evidence that the availably abundant water could affect the distribution of oxygenated organic compounds produced in the oxidation of volatile organic compounds.


2014 ◽  
Vol 7 (1) ◽  
pp. 379-429 ◽  
Author(s):  
F. Couvidat ◽  
K. Sartelet

Abstract. The Secondary Organic Aerosol Processor (SOAP v1.0) model is presented. This model is designed to be modular with different user options depending on the computing time and the complexity required by the user. This model is based on the molecular surrogate approach, in which each surrogate compound is associated with a molecular structure to estimate some properties and parameters (hygroscopicity, absorption on the aqueous phase of particles, activity coefficients, phase separation). Each surrogate can be hydrophilic (condenses only on the aqueous phase of particles), hydrophobic (condenses only on the organic phase of particles) or both (condenses on both the aqueous and the organic phases of particles). Activity coefficients are computed with the UNIFAC thermodynamic model for short-range interactions and with the AIOMFAC parameterization for medium and long-range interactions between electrolytes and organic compounds. Phase separation is determined by Gibbs energy minimization. The user can choose between an equilibrium and a dynamic representation of the organic aerosol. In the equilibrium representation, compounds in the particle phase are assumed to be at equilibrium with the gas phase. However, recent studies show that the organic aerosol (OA) is not at equilibrium with the gas phase because the organic phase could be semi-solid (very viscous liquid phase). The condensation or evaporation of organic compounds could then be limited by the diffusion in the organic phase due to the high viscosity. A dynamic representation of secondary organic aerosols (SOA) is used with OA divided into layers, the first layer at the center of the particle (slowly reaches equilibrium) and the final layer near the interface with the gas phase (quickly reaches equilibrium).


2015 ◽  
Vol 8 (4) ◽  
pp. 1111-1138 ◽  
Author(s):  
F. Couvidat ◽  
K. Sartelet

Abstract. In this paper the Secondary Organic Aerosol Processor (SOAP v1.0) model is presented. This model determines the partitioning of organic compounds between the gas and particle phases. It is designed to be modular with different user options depending on the computation time and the complexity required by the user. This model is based on the molecular surrogate approach, in which each surrogate compound is associated with a molecular structure to estimate some properties and parameters (hygroscopicity, absorption into the aqueous phase of particles, activity coefficients and phase separation). Each surrogate can be hydrophilic (condenses only into the aqueous phase of particles), hydrophobic (condenses only into the organic phases of particles) or both (condenses into both the aqueous and the organic phases of particles). Activity coefficients are computed with the UNIFAC (UNIversal Functional group Activity Coefficient; Fredenslund et al., 1975) thermodynamic model for short-range interactions and with the Aerosol Inorganic–Organic Mixtures Functional groups Activity Coefficients (AIOMFAC) parameterization for medium- and long-range interactions between electrolytes and organic compounds. Phase separation is determined by Gibbs energy minimization. The user can choose between an equilibrium representation and a dynamic representation of organic aerosols (OAs). In the equilibrium representation, compounds in the particle phase are assumed to be at equilibrium with the gas phase. However, recent studies show that the organic aerosol is not at equilibrium with the gas phase because the organic phases could be semi-solid (very viscous liquid phase). The condensation–evaporation of organic compounds could then be limited by the diffusion in the organic phases due to the high viscosity. An implicit dynamic representation of secondary organic aerosols (SOAs) is available in SOAP with OAs divided into layers, the first layer being at the center of the particle (slowly reaches equilibrium) and the final layer being near the interface with the gas phase (quickly reaches equilibrium). Although this dynamic implicit representation is a simplified approach to model condensation–evaporation with a low number of layers and short CPU (central processing unit) time, it shows good agreements with an explicit representation of condensation–evaporation (no significant differences after a few hours of condensation).


2020 ◽  
Author(s):  
Simon Rosanka ◽  
Rolf Sander ◽  
Bruno Franco ◽  
Catherine Wespes ◽  
Andreas Wahner ◽  
...  

Abstract. In liquid cloud droplets, superoxide anion (O−2(aq)) is known to quickly consume ozone (O3(aq)), which is relatively insoluble. The significance of this reaction as tropospheric O3 sink is sensitive to the abundance of O−2(aq) and therefore to the production of its main precursor, hydroperoxyl radical (HO2(aq)). The aqueous-phase oxidation of oxygenated volatile organic compounds (OVOCs) is the major source of HO2(aq) in cloud droplets. Hence, the lack of explicit aqueous-phase chemical kinetics in global atmospheric models leads to a general underestimation of clouds as O3 sinks. In this study, the importance of in-cloud OVOC oxidation for tropospheric composition is assessed by using the Chemistry As A Boxmodel Application (CAABA) and the global atmospheric model ECHAM/MESSy (EMAC), which are both capable of explicitly representing the relevant chemical transformations. For this analysis, three different in-cloud oxidation mechanisms are employed: (1) one including the basic oxidation of SO2(aq) via O3(aq) and H2O2(aq), which thus represents the capabilities of most global models, (2) the more advanced standard EMAC mechanism, which includes inorganic chemistry and simplified degradation of methane oxidation products, and (3) the detailed in-cloud OVOC oxidation scheme Jülich Aqueous-phase Mechanism of Organic Chemistry (JAMOC). By using EMAC, the global impact of each mechanism is assessed focusing mainly on tropospheric volatile organic compounds (VOCs), HOx (HOx = OH+HO2), and O3. This is achieved by performing a detailed HOx and O3 budget analysis in the gas- and aqueous-phase. The resulting changes are evaluated against O3 and methanol (CH3OH) satellite observations from the Infrared Atmospheric Sounding Interferometer (IASI) for 2015. In general, the explicit in-cloud oxidation leads to an overall reduction of predicted OVOCs levels, and reduces EMAC's overestimation of some OVOCs in the tropics. The in-cloud OVOC oxidation shifts the HO2 production from the gas- to the aqueous-phase. As a result, the O3 budget is perturbed with scavenging being enhanced and the gas-phase chemical losses being reduced. With the simplified in-cloud chemistry, about 13 Tg a−1 of O3 are scavenged, which increases to 336 Tg a−1 when JAMOC is used. The highest O3 reduction of 12 % is predicted in the upper troposphere/lower stratosphere (UTLS). These changes in the free troposphere significantly reduce the modelled tropospheric ozone columns, which are known to be generally overestimated by EMAC and other global atmospheric models.


2016 ◽  
Author(s):  
Camille Mouchel-Vallon ◽  
Laurent Deguillaume ◽  
Anne Monod ◽  
Hélène Perroux ◽  
Clémence Rose ◽  
...  

Abstract. Organic compounds of both anthropogenic and natural origin are ubiquitous in the multiphasic atmospheric medium. Their transformation in the atmosphere affects air quality and the global climate. Modelling provides a useful tool to investigate the chemistry of organic compounds in the tropospheric multiphase system. While several comprehensive explicit mechanisms exist in the gas phase, explicit mechanisms are much more limited in the aqueous phase. Recently, new empirical methods have been developed to estimate HO• reaction rates in the aqueous phase: structure-activity relationships (SARs) provide global rate constants and branching ratios for HO• abstraction from and addition to atmospheric organic compounds. Based on these SARs, a new detailed aqueous-phase mechanism, named the cloud explicit physico-chemical scheme (CLEPS), to describe the oxidation of hydrosoluble organic compounds resulting from isoprene oxidation is proposed. In this paper, a protocol based on reviewed experimental data and evaluated prediction methods is described in detail. The current version of the mechanism includes approximately 850 aqueous reactions and 465 equilibria. Inorganic reactivity is described for 67 chemical species (e.g., transition metal ions, HxOy, sulphur species, nitrogen species, and chlorine). For organic compounds, 87 chemical species are considered in the mechanism, corresponding to 657 chemical forms that are individually followed (e.g., hydrated forms, anionic forms). This new aqueous-phase mechanism is coupled with the detailed gas phase mechanism MCM v3.3.1 through mass transfer parameterization for the exchange between the gas phase and aqueous phase. The GROMHE SAR enables the evaluation of the Henry's law constants for undocumented organic compounds. The resulting multiphase mechanism is implemented in a model based on the Dynamically Simple Model for Atmospheric Chemical Complexity (DSMACC) using the Kinetic PreProcessor (KPP). This model allows simulation of the time evolution of the concentrations of each individual chemical species in addition to detailed time-resolved flux analyses. The variable photolysis in both phases is calculated using the TUV 4.5 radiative transfer model. To evaluate our chemical mechanism, an idealized cloud event with fixed microphysical cloud parameters is simulated. The simulation is performed for a low-NOx situation. The results indicate the formation of oxidized mono- and diacids in the aqueous phase, as well as a significant influence on the gas phase chemistry and composition. For this particular simulation, the aqueous phase mechanism is responsible for the efficient fragmentation and functionalization of organic compounds. This new cloud chemistry model allows for the analysis of individual aqueous sub systems and can be used to analyze the results from cloud chamber experiments and field campaigns.


2021 ◽  
Author(s):  
Majda Mekic ◽  
Thomas Schaefer ◽  
Hartmut Herrmann

<p>Anthropogenic and biogenic sources produce numerous primary emitted gases, organic compounds, and aerosols in the atmosphere. An important group of such compounds are α, β-unsaturated carbonyl molecules, which can be formed in the atmosphere due to their secondary origin, including oxidation of their precursors such as hydrocarbons with common atmospheric oxidants such as hydroxyl radicals (‧OH). Since those compounds contain at least one double bond and one carbonyl group, they are characterized as water-soluble molecules, which can diffuse on the cloud droplets’ surface and undergo a phase transfer from the gas phase to the atmospheric aqueous phase. In the latter, the oxidized organic compounds can contribute to aerosol mass production through in-cloud processes, yielding aqueous phase secondary organic aerosols (aqSOA). Due to their strong photochemical behavior, the development of a new analytical approach for evaluating the OH radical kinetics in the aqueous phase under dark conditions was essential. One of the most studied non-photolytic reactions is Fenton chemistry (Fe(II)/H<sub>2</sub>O<sub>2</sub>), which serves as an OH radical source in the dark in the atmospheric aqueous phase after catalytic decomposition of H<sub>2</sub>O<sub>2</sub> in the presence of Fe(II) at acidic pH values. In a typical experiment, temperature-dependent second-order rate constants of OH radicals with unsaturated dialdehydes, such as (1) crotonaldehyde, and (2) 1,4-butenedial, were determined in a bulk reactor by using the competition kinetics method. In the newly developed method, the role of radical scavenger was performed by isotopically labeled 2-propanol (d8), while the OH-initiated oxidation produces deuterated acetone (d6), being analyzed with GC-MS after derivatization. The findings from our research will be incorporated in the CAPRAM model to explain discrepancies between experimentally observed and predicted aqSOA properties.</p>


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