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

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.

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

10.5194/acp-2018-1318 ◽

2019 ◽

Author(s):

Peter Bräuer ◽

Camille Mouchel-Vallon ◽

Andreas Tilgner ◽

Anke Mutzel ◽

Olaf Böge ◽

...

Keyword(s):

Organic Compounds ◽

Aqueous Phase ◽

Rate Constants ◽

Particle Growth ◽

Estimation Methods ◽

Radical Reactivity ◽

Chemical Complexity ◽

Model Studies ◽

Aerosol Chamber ◽

Phase Chemistry

Abstract. This paper presents a new CAPRAM/GECKO-A protocol for mechanism auto-generation of aqueous-phase organic mechanisms. For the development, kinetic data in the literature was 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 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 enthalpy (BDE). The improved Evans-Polanyi-type correlations are used to predict rate constants for aqueous-phase NO3 + organic compounds reactions. Extensive tests have been performed on essential parameters and 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 mesitylene oxidation experiment has been performed at the aerosol chamber LEAK at high relative humidity conditions and compared to a multiphase mechanism using the MCMv3.2 in the gas phase and 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 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 supplementary tool for aerosol chambers to design and analyse experiments of chemical complexity and help understanding them on a molecular level.

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

10.5194/egusphere-egu21-10276 ◽

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

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 J&#252;lich 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.&#160;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 (HO2) production from the gas- to the aqueous-phase. As a result, the in-cloud destruction (scavenging) of ozone (O3) by the superoxide anion (O2-) is enhanced and accompanied by a reduction in both sources and sinks of tropospheric O3 in the gas phase. By considering only the in-cloud sulfur oxidation by O3, about 13 Tg a-1 of O3 are scavenged, which increases to 336 Tg a-1 when JAMOC is used. With the full oxidation scheme, the highest O3 reduction of 12 % is predicted in the upper troposphere/lower stratosphere (UTLS). Based on the IASI O3 retrievals, it is demonstrated that these changes in the free troposphere significantly reduce the modelled tropospheric O3 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. &#160;

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

Geoscientific Model Development ◽

10.5194/gmd-10-1339-2017 ◽

2017 ◽

Vol 10 (3) ◽

pp. 1339-1362 ◽

Cited By ~ 15

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.

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Oxidation of substituted aromatic hydrocarbons in the tropospheric aqueous phase: kinetic mechanism development and modelling

Physical Chemistry Chemical Physics ◽

10.1039/c7cp08576a ◽

2018 ◽

Vol 20 (16) ◽

pp. 10960-10977 ◽

Cited By ~ 17

Author(s):

Erik H. Hoffmann ◽

Andreas Tilgner ◽

Ralf Wolke ◽

Olaf Böge ◽

Arno Walter ◽

...

Keyword(s):

Aqueous Phase ◽

Aromatic Hydrocarbons ◽

Aromatic Compounds ◽

Kinetic Data ◽

Kinetic Mechanism ◽

Detailed Model ◽

Model Studies ◽

Phase Chemistry

An aqueous-phase chemistry mechanism for the oxidation of aromatic compounds in the atmosphere is developed based on available kinetic data. Detailed model studies successfully describe the oxidation and functionalization of monoaromatic compounds in the atmosphere.

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Radical mechanisms of methyl vinyl ketone oligomerization through aqueous phase OH-oxidation: on the paradoxical role of dissolved molecular oxygen

Atmospheric Chemistry and Physics Discussions ◽

10.5194/acpd-13-2913-2013 ◽

2013 ◽

Vol 13 (1) ◽

pp. 2913-2954 ◽

Cited By ~ 2

Author(s):

P. Renard ◽

F. Siekmann ◽

A. Gandolfo ◽

J. Socorro ◽

G. Salque ◽

...

Keyword(s):

Aqueous Phase ◽

High Resolution Mass Spectrometry ◽

Organic Aerosol ◽

Vinyl Ketone ◽

Methyl Vinyl Ketone ◽

Chemical Mechanism ◽

Methyl Vinyl ◽

Phase Chemistry ◽

Dissolved O2

Abstract. It is now accepted that one of the important pathways of Secondary Organic Aerosol (SOA) formation occurs through aqueous phase chemistry in the atmosphere. However, the liquid phase chemical mechanisms leading to macromolecules are still not well understood. For α-dicarbonyl precursors, such as methylglyoxal and glyoxal, radical reactions through OH-oxidation produce oligomers, irreversibly and faster than accretion reactions. Methyl vinyl ketone (MVK) was chosen in the present study as it is an α, β-unsaturated carbonyl that can undergo such reaction pathways in the aqueous phase and forms even high molecular weight oligomers. We present here experiments on the aqueous phase OH-oxidation of MVK, performed under atmospheric relevant conditions. Using NMR and UV absorption spectroscopy, high and ultra-high resolution mass spectrometry, we show that the fast formation of oligomers up to 1800 Da is due to radical oligomerization of MVK, and 13 series of oligomers (out of a total of 26 series) are identified. The influence of atmospherically relevant parameters such as temperature, initial concentrations of MVK and dissolved oxygen are presented and discussed. In agreement with the experimental observations, we propose a chemical mechanism of OH-oxidation of MVK in the aqueous phase that proceeds via radical oligomerization of MVK on the olefin part of the molecule. This mechanism highlights the paradoxical role of dissolved O2: while it inhibits oligomerization reactions, it contributes to produce oligomerization initiator radicals, which rapidly consume O2, thus leading to the supremacy of oligomerization reactions after several minutes of reaction. These processes, together with the large ranges of initial concentrations investigated (60–656 μM of dissolved O2 and 0.2–20 mM of MVK) show the fundamental role that O2 likely plays in atmospheric organic aerosol.

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

Atmospheric Chemistry and Physics ◽

10.5194/acp-19-13741-2019 ◽

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.

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Functionalization and fragmentation during ambient organic aerosol aging: application of the 2-D volatility basis set to field studies

Atmospheric Chemistry and Physics Discussions ◽

10.5194/acpd-12-9857-2012 ◽

2012 ◽

Vol 12 (4) ◽

pp. 9857-9901 ◽

Cited By ~ 1

Author(s):

B. N. Murphy ◽

N. M. Donahue ◽

C. Fountoukis ◽

M. Dall'Osto ◽

C. O'Dowd ◽

...

Keyword(s):

Organic Compounds ◽

Aqueous Phase ◽

Transport Model ◽

Field Studies ◽

Organic Aerosol ◽

Basis Set ◽

Base Case ◽

Chemical Transport Model ◽

Heterogeneous Oxidation ◽

Phase Chemistry

Abstract. Multigenerational oxidation chemistry of atmospheric organic compounds and its effects on aerosol loadings and chemical composition is investigated by implementing the Two-Dimensional Volatility Basis Set (2-D-VBS) in a Lagrangian host chemical transport model. Three model formulations were chosen to explore the complex interactions between functionalization and fragmentation processes during gas-phase oxidation of organic compounds by the hydroxyl radical. The base case model employs a conservative transformation by assuming a reduction of one order of magnitude in effective saturation concentration and an increase of oxygen content by one or two oxygen atoms per oxidation generation. A second scheme simulates functionalization in more detail using group contribution theory to estimate the effects of oxygen addition to the carbon backbone on the compound volatility. Finally, a fragmentation scheme is added to the detailed functionalization scheme to create a functionalization-fragmentation parameterization. Two condensed-phase chemistry pathways are also implemented as additional sensitivity tests to simulate (1) heterogeneous oxidation via OH uptake to the particle-phase and (2) aqueous-phase chemistry of glyoxal and methylglyoxal. The model is applied to summer and winter periods at three sites where observations of organic aerosol (OA) mass and O:C were obtained during the European Integrated Project on Aerosol Cloud Climate and Air Quality Interactions (EUCAARI) campaigns. The base case model reproduces observed mass concentrations and O:C well, with fractional errors (FE) lower than 55% and 25%, respectively. The detailed functionalization scheme tends to overpredict OA concentrations, especially in the summertime, and also underpredicts O:C by approximately a factor of 2. The detailed functionalization model with fragmentation agrees well with the observations for OA concentration, but still underpredicts O:C. Both heterogeneous oxidation and aqueous-phase processing have small effects on OA levels but heterogeneous oxidation, as implemented here, does enhance O:C by about 0.1. The different schemes result in very different fractional attribution for OA between anthropogenic and biogenic sources.

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An advanced modeling study on the impacts and atmospheric implications of multiphase dimethyl sulfide chemistry

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1606320113 ◽

2016 ◽

Vol 113 (42) ◽

pp. 11776-11781 ◽

Cited By ~ 61

Author(s):

Erik Hans Hoffmann ◽

Andreas Tilgner ◽

Roland Schrödner ◽

Peter Bräuer ◽

Ralf Wolke ◽

...

Keyword(s):

Aqueous Phase ◽

Dimethyl Sulfide ◽

Oxidation Products ◽

Radical Mechanism ◽

Sulfur Source ◽

Aerosol Formation ◽

Detailed Model ◽

Model Studies ◽

Dms Oxidation ◽

Phase Chemistry

Oceans dominate emissions of dimethyl sulfide (DMS), the major natural sulfur source. DMS is important for the formation of non-sea salt sulfate (nss-SO42−) aerosols and secondary particulate matter over oceans and thus, significantly influence global climate. The mechanism of DMS oxidation has accordingly been investigated in several different model studies in the past. However, these studies had restricted oxidation mechanisms that mostly underrepresented important aqueous-phase chemical processes. These neglected but highly effective processes strongly impact direct product yields of DMS oxidation, thereby affecting the climatic influence of aerosols. To address these shortfalls, an extensive multiphase DMS chemistry mechanism, the Chemical Aqueous Phase Radical Mechanism DMS Module 1.0, was developed and used in detailed model investigations of multiphase DMS chemistry in the marine boundary layer. The performed model studies confirmed the importance of aqueous-phase chemistry for the fate of DMS and its oxidation products. Aqueous-phase processes significantly reduce the yield of sulfur dioxide and increase that of methyl sulfonic acid (MSA), which is needed to close the gap between modeled and measured MSA concentrations. Finally, the simulations imply that multiphase DMS oxidation produces equal amounts of MSA and sulfate, a result that has significant implications for nss-SO42− aerosol formation, cloud condensation nuclei concentration, and cloud albedo over oceans. Our findings show the deficiencies of parameterizations currently used in higher-scale models, which only treat gas-phase chemistry. Overall, this study shows that treatment of DMS chemistry in both gas and aqueous phases is essential to improve the accuracy of model predictions.

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