scholarly journals Oxidation of low-molecular weight organic compounds in cloud droplets: development of the JAMOC chemical mechanism in CAABA/MECCA (version 4.5.0gmdd)

2020 ◽  
Author(s):  
Simon Rosanka ◽  
Rolf Sander ◽  
Andreas Wahner ◽  
Domenico Taraborrelli
Keyword(s):  
Gas Phase ◽  
Organic Compounds ◽  
Aqueous Phase ◽  
Phase Transfer ◽  
Chemical Mechanism ◽  
Cloud Droplets ◽  
Physico Chemical ◽  
Chemical Scheme ◽  
Selection Of Species ◽  
Bug Fixes

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.

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
Keyword(s):  
Organic Chemistry ◽  
Gas Phase ◽  
Organic Compounds ◽  
Aqueous Phase ◽  
Phase Transfer ◽  
Cloud Droplets ◽  
Physico Chemical ◽  
Oxygenated Volatile Organic Compounds ◽  
Chemical Scheme ◽  
Selection Of Species

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.

scholarly journals CLEPS 1.0: A new protocol for cloud aqueous phase oxidation of VOC mechanisms

2017 ◽  
Vol 10 (3) ◽  
pp. 1339-1362 ◽  
Author(s):  
Camille Mouchel-Vallon ◽  
Laurent Deguillaume ◽  
Anne Monod ◽  
Hélène Perroux ◽  
Clémence Rose ◽  
...  
Keyword(s):  
Gas Phase ◽  
Organic Compounds ◽  
Aqueous Phase ◽  
Water Soluble ◽  
Transfer Scheme ◽  
Chemical Complexity ◽  
Global Rate ◽  
Physico Chemical ◽  
Chemical Scheme ◽  
Phase Chemistry

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.

Influence of in-cloud oxidation of organic compounds on tropospheric ozone

2021 ◽  
Author(s):  
Simon Rosanka ◽  
Rolf Sander ◽  
Bruno Franco ◽  
Catherine Wespes ◽  
Andreas Wahner ◽  
...  
Keyword(s):  
Gas Phase ◽  
Organic Compounds ◽  
Aqueous Phase ◽  
Phase Transfer ◽  
Sulfur Oxidation ◽  
Box Model ◽  
Atmospheric Models ◽  
Model Studies ◽  
Phase Chemistry ◽  
The Impact

<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>

scholarly journals CLEPS: A new protocol for cloud aqueous phase oxidation of VOC mechanisms

2016 ◽  
Author(s):  
Camille Mouchel-Vallon ◽  
Laurent Deguillaume ◽  
Anne Monod ◽  
Hélène Perroux ◽  
Clémence Rose ◽  
...  
Keyword(s):  
Gas Phase ◽  
Organic Compounds ◽  
Aqueous Phase ◽  
Chemical Species ◽  
Transition Metal Ions ◽  
Reaction Rates ◽  
Chemical Mechanism ◽  
Multiphase System ◽  
Transfer Model ◽  
Climate Modelling

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.

scholarly journals Explicit modeling of volatile organic compounds partitioning in the atmospheric aqueous phase

2013 ◽  
Vol 13 (2) ◽  
pp. 1023-1037 ◽  
Author(s):  
C. Mouchel-Vallon ◽  
P. Bräuer ◽  
M. Camredon ◽  
R. Valorso ◽  
S. Madronich ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Water Content ◽  
Gas Phase ◽  
Aqueous Phase ◽  
Water Soluble ◽  
Chemical Mechanism ◽  
Organic Species ◽  
Cloud Water Content ◽  
Isoprene Oxidation

Abstract. The gas phase oxidation of organic species is a multigenerational process involving a large number of secondary compounds. Most secondary organic species are water-soluble multifunctional oxygenated molecules. The fully explicit chemical mechanism GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere) is used to describe the oxidation of organics in the gas phase and their mass transfer to the aqueous phase. The oxidation of three hydrocarbons of atmospheric interest (isoprene, octane and α-pinene) is investigated for various NOx conditions. The simulated oxidative trajectories are examined in a new two dimensional space defined by the mean oxidation state and the solubility. The amount of dissolved organic matter was found to be very low (yield less than 2% on carbon atom basis) under a water content typical of deliquescent aerosols. For cloud water content, 50% (isoprene oxidation) to 70% (octane oxidation) of the carbon atoms are found in the aqueous phase after the removal of the parent hydrocarbons for low NOx conditions. For high NOx conditions, this ratio is only 5% in the isoprene oxidation case, but remains large for α-pinene and octane oxidation cases (40% and 60%, respectively). Although the model does not yet include chemical reactions in the aqueous phase, much of this dissolved organic matter should be processed in cloud drops and modify both oxidation rates and the speciation of organic species.

scholarly journals Aerosol mass yields of selected biogenic volatile organic compounds – a theoretical study with nearly explicit gas-phase chemistry

2019 ◽  
Vol 19 (22) ◽  
pp. 13741-13758
Author(s):  
Carlton Xavier ◽  
Anton Rusanen ◽  
Putian Zhou ◽  
Chen Dean ◽  
Lukas Pichelstorfer ◽  
...  
Keyword(s):  
Volatile Organic Compounds ◽  
Gas Phase ◽  
Organic Compounds ◽  
Chemical Mechanism ◽  
Biogenic Volatile Organic Compounds ◽  
Gas Phase Chemistry ◽  
Mass Load ◽  
Volatile Organic ◽  
Phase Chemistry ◽  
Good Agreement

Abstract. In this study we modeled secondary organic aerosol (SOA) mass loadings from the oxidation (by O3, OH and NO3) of five representative biogenic volatile organic compounds (BVOCs): isoprene, endocyclic bond-containing monoterpenes (α-pinene and limonene), exocyclic double-bond compound (β-pinene) and a sesquiterpene (β-caryophyllene). The simulations were designed to replicate an idealized smog chamber and oxidative flow reactors (OFRs). The Master Chemical Mechanism (MCM) together with the peroxy radical autoxidation mechanism (PRAM) were used to simulate the gas-phase chemistry. The aim of this study was to compare the potency of MCM and MCM + PRAM in predicting SOA formation. SOA yields were in good agreement with experimental values for chamber simulations when MCM + PRAM was applied, while a stand-alone MCM underpredicted the SOA yields. Compared to experimental yields, the OFR simulations using MCM + PRAM yields were in good agreement for BVOCs oxidized by both O3 and OH. On the other hand, a stand-alone MCM underpredicted the SOA mass yields. SOA yields increased with decreasing temperatures and NO concentrations and vice versa. This highlights the limitations posed when using fixed SOA yields in a majority of global and regional models. Few compounds that play a crucial role (>95 % of mass load) in contributing to SOA mass increase (using MCM + PRAM) are identified. The results further emphasized that incorporating PRAM in conjunction with MCM does improve SOA mass yield estimation.

scholarly journals The number fraction of iron-containing particles affects OH, HO<sub>2</sub> and H<sub>2</sub>O<sub>2</sub> budgets in the atmospheric aqueous phase

2021 ◽  
Author(s):  
Amina Khaled ◽  
Minghui Zhang ◽  
Barbara Ervens
Keyword(s):  
Particulate Matter ◽  
Aqueous Phase ◽  
Aerosol Particles ◽  
Iron Concentration ◽  
Transition Metal Ions ◽  
Total Iron ◽  
Chemical Mechanism ◽  
Cloud Droplets ◽  
Iron Distribution ◽  
Total Iron Concentration

Abstract. Reactive oxygen species (ROS), such as OH, HO2, H2O2 affect the oxidation capacity of the atmosphere and cause adverse health effects of particulate matter. The role of transition metal ions (TMIs) in impacting the ROS concentrations and conversions in the atmospheric aqueous phase has been recognized for a long time. Model studies usually assume that the total TMI concentration as measured in bulk aerosol or cloud water samples is distributed equally across all particles or droplets. This assumption is contrary to single-particle measurements that have shown that only a small number fraction of particles contain iron and other TMIs (FN,Fe < 100 %) which implies that also not all cloud droplets contain TMIs. In the current study, we apply a box model with an explicit multiphase chemical mechanism to simulate ROS formation and cycling in (i) aqueous aerosol particles and (ii) cloud droplets. Model simulations are performed for the range of 1 % ≤ FN,Fe ≤ 100 % for constant pH values of 3, 4.5 and 6 and constant total iron concentration (10 or 50 . Model results are compared for two sets of simulations with FN,Fe < 100 % (FeN < 100) and 100 % (FeBulk). We find largest differences between model results in OH and HO2/O2− concentrations at pH = 6. Under these conditions, HO2 is subsaturated in the aqueous phase because of its high effective Henry's law constant and the fast chemical loss reactions of the O2− radical anion. As the main reduction of process of Fe(III) is its reaction with HO2/O2−, we show that the HO2 subsaturation leads to predicted Fe(II)/Fe(total) ratios for FN,Fe < 100 % that are lower by a factor of ≤ 2 as compared to bulk model approaches. This trend is largely independent of the total iron concentration, as both chemical source and sink rates of HO2/O2− scale with the iron concentration. The chemical radical (OH, HO2) loss in particles is usually compensated by its uptake from the gas phase. We compare model-derived reactive uptake parameters γ(OH) and γ(HO2) for the full range of FN,Fe. While γ(OH) is not affected by the iron distribution, the calculated γ(HO2) range from 0.0004 to 0.03 for FN,Fe = 1 % and 100 %, respectively. Implications of these findings are discussed for the application of lab-derived γ(HO2) in models to present reactive HO2 uptake on aerosols. As the oxidant budget in aerosol particles and cloud droplets is related to the oxidative potential, we also conclude that the iron distribution FN,Fe should be taken into account to estimate the ROS concentrations and health impacts of particulate matter that might be overestimated by bulk sampling and model approaches. Our study suggests that the number concentration of iron-containing particles may be more important than the total iron mass concentration in determining ROS budgets and uptake rates in cloud and aerosol water.

scholarly journals Development of a protocol for the auto-generation of explicit aqueous-phase oxidation schemes of organic compounds

2019 ◽  
Vol 19 (14) ◽  
pp. 9209-9239 ◽  
Author(s):  
Peter Bräuer ◽  
Camille Mouchel-Vallon ◽  
Andreas Tilgner ◽  
Anke Mutzel ◽  
Olaf Böge ◽  
...  
Keyword(s):  
Organic Compounds ◽  
Aqueous Phase ◽  
Rate Constants ◽  
Particle Growth ◽  
Chemical Mechanism ◽  
Estimation Methods ◽  
Radical Reactivity ◽  
Chemical Complexity ◽  
Model Studies ◽  
Phase Chemistry

Abstract. This paper presents a new CAPRAM–GECKO-A protocol for mechanism auto-generation of aqueous-phase organic processes. For the development, kinetic data in the literature were reviewed and a database with 464 aqueous-phase reactions of the hydroxyl radical with organic compounds and 130 nitrate radical reactions with organic compounds has been compiled and evaluated. Five different methods to predict aqueous-phase rate constants have been evaluated with the help of the kinetics database: gas–aqueous phase correlations, homologous series of various compound classes, radical reactivity comparisons, Evans–Polanyi-type correlations, and structure–activity relationships (SARs). The quality of these prediction methods was tested as well as their suitability for automated mechanism construction. Based on this evaluation, SARs form the basis of the new CAPRAM–GECKO-A protocol. Evans–Polanyi-type correlations have been advanced to consider all available H atoms in a molecule besides the H atoms with only the weakest bond dissociation enthalpies (BDEs). The improved Evans–Polanyi-type correlations are used to predict rate constants for aqueous-phase NO3 and organic compounds reactions. Extensive tests have been performed on essential parameters and on highly uncertain parameters with limited experimental data. These sensitivity studies led to further improvements in the new CAPRAM–GECKO-A protocol but also showed current limitations. Biggest uncertainties were observed in uptake processes and the estimation of Henry's law coefficients as well as radical chemistry, in particular the degradation of alkoxy radicals. Previous estimation methods showed several deficits, which impacted particle growth. For further evaluation, a 1,3,5-trimethylbenzene oxidation experiment has been performed in the aerosol chamber “Leipziger Aerosolkammer” (LEAK) at high relative humidity conditions and compared to a multiphase mechanism using the Master Chemical Mechanism (MCMv3.2) in the gas phase and using a methylglyoxal oxidation scheme of about 600 reactions generated with the new CAPRAM–GECKO-A protocol in the aqueous phase. While it was difficult to evaluate single particle constituents due to concentrations close to the detection limits of the instruments applied, the model studies showed the importance of aqueous-phase chemistry in respect to secondary organic aerosol (SOA) formation and particle growth. The new protocol forms the basis for further CAPRAM mechanism development towards a new version 4.0. Moreover, it can be used as a supplementary tool for aerosol chambers to design and analyse experiments of chemical complexity and help to understand them on a molecular level.

scholarly journals The kinetics and mechanism of an aqueous phase isoprene reaction with hydroxyl radical

2011 ◽  
Vol 11 (15) ◽  
pp. 7399-7415 ◽  
Author(s):  
D. Huang ◽  
X. Zhang ◽  
Z. M. Chen ◽  
Y. Zhao ◽  
X. L. Shen
Keyword(s):  
Oxalic Acid ◽  
Gas Phase ◽  
Organic Compounds ◽  
Aqueous Phase ◽  
Laboratory Simulation ◽  
Potential Contribution ◽  
Phase Reaction ◽  
Oh Radical ◽  
Reaction Products ◽  
Isoprene Oxidation

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.

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