Efficient implementation of advanced Richardson Extrapolation in an atmospheric chemical scheme

The numerical treatment of an atmospheric chemical scheme, which contains 56 species, is discussed in this paper. This scheme is often used in studies of air pollution levels in different domains, as, for example, in Europe, by large-scale environmental models containing additionally two other important physical processes—transport of pollutants in the atmosphere (advection) and diffusion phenomena. We shall concentrate our attention on the efficient numerical treatment of the chemical scheme by using Implicit Runge–Kutta Methods combined with accurate and efficient advanced versions of the Richardson Extrapolation. A Variable Stepsize Variable Formula Method is developed in order to achieve high accuracy of the calculated results within a reasonable computational time. Reliable estimations of the computational errors when the proposed numerical methods are used in the treatment of the chemical scheme will be demonstrated by presenting results from several representative runs and comparing these results with “exact” concentrations obtained by applying a very small stepsize during the computations. Results related to the diurnal variations of some of the chemical species will also be presented. The approach used in this paper does not depend on the particular chemical scheme and can easily be applied when other atmospheric chemical schemes are selected.

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)

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.

The impact of inhomogeneous emissions and topography on ozone photochemistry in the vicinity of Hong Kong Island

Global and regional chemical transport models of the atmosphere are based on the assumption that chemical species are completely mixed within each model grid box. However, in reality, these species are often segregated due to localized sources and the influence of topography. In order to investigate the degree to which the rates of chemical reactions between two reactive species are reduced due to the possible segregation of species within the convective boundary layer, we perform large-eddy simulations (LESs) in the mountainous region of Hong Kong Island. We adopt a simple chemical scheme with 15 primary and secondary chemical species, including ozone and its precursors. We calculate the segregation intensity due to inhomogeneity in the surface emissions of primary pollutants and due to turbulent motions related to topography. We show that the inhomogeneity in the emissions increases the segregation intensity by a factor of 2–5 relative to a case in which the emissions are assumed to be uniformly distributed. Topography has an important effect on the segregation locally, but this influence is relatively limited when considering the spatial domain as a whole. In the particular setting of our model, segregation reduces the ozone formation by 8 %–12 % compared to the case with complete mixing, implying that the coarse-resolution models may overestimate the surface ozone when ignoring the segregation effect.

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

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.

The impact of inhomogeneous emissions and topography on ozone photochemistry in the vicinity of the Hong Kong island

Global and regional chemical transport models of the atmosphere are based on the assumption that chemical species are completely mixed within each model grid box. However, in reality, these species are often segregated due to localized sources and the influence of the topography. In order to investigate the degree to which the rates of chemical reactions between two reactive species are reduced due to the possible segregation of species within the convective boundary layer, we perform large-eddy simulations (LES) in the mountainous region of the Hong Kong island. We adopt a simple chemical scheme with 15 primary and secondary chemical species including ozone and its precursors. We calculate the segregation intensity due to inhomogeneity in the surface emissions of primary pollutants and due to turbulent motions related to topography. We show that the inhomogeneity in the emissions increases the segregation intensity by a factor 2–5 relative to a case in which the emissions are assumed to be uniformly distributed. Topography has an important effect on the segregation locally, but this influence is relatively limited when considering the spatial domain as a whole.

New chemical scheme for giant planet thermochemistry

Context. Several chemical networks have been developed to study warm (exo)planetary atmospheres. The kinetics of the reactions related to the methanol chemistry included in these schemes have been questioned. Aims. The goal of this paper is to update the methanol chemistry for such chemical networks based on recent publications in the combustion literature. We also aim to study the consequences of this update on the atmospheric compositions of (exo)planetary atmospheres and brown dwarfs. Methods. We performed an extensive review of combustion experimental studies and revisited the sub-mechanism describing methanol combustion in a scheme published in 2012. The updated scheme involves 108 species linked by a total of 1906 reactions. We then applied our 1D kinetic model with this new scheme to the case studies HD 209458b, HD 189733b, GJ 436b, GJ 1214b, ULAS J1335+11, Uranus, and Neptune; we compared these results with those obtained with the former scheme. Results. The update of the scheme has a negligible impact on the atmospheres of hot Jupiters. However, the atmospheric composition of warm Neptunes and brown dwarfs is modified sufficiently to impact observational spectra in the wavelength range in which James Webb Space Telescope will operate. Concerning Uranus and Neptune, the update of the chemical scheme modifies the abundance of CO and thus impacts the deep oxygen abundance required to reproduce the observational data. For future 3D kinetics models, we also derived a reduced scheme containing 44 species and 582 reactions. Conclusions. Chemical schemes should be regularly updated to maintain a high level of reliability on the results of kinetic models and be able to improve our knowledge of planetary formation.

Kinetics of catalytic oxidation 4-bromethylbenzene by ozone in acetic acid

The kinetic regularities of catalytic oxidation of 4-bromoethylbenzene by ozone to create an eco-logical, low-temperature technology for the synthesis of 4-bromoacetophenone have been studied. The experiment was performed in a glass reactor with a porous membrane under conditions of kinetic regime at a temperature of 293-333 K. The concentration of ozone in the gas phase was determined by spectrophotometric method. Analysis of 4-bromoacetophenone and its oxidation products was performed by gas-liquid chromatography. Oxidation of 4-bromoethylbenzene by ozone in a solution of acetic acid at a temperature of 293 K in the presence of catalytic impurities of manganese (II) ace-tate proceeds mainly on the ethyl group with the formation of a mixture of 4-bromoacetophenone (95.6 %) and 1-(4-bromophenylethanoacetate 4.2 % ). Prevention of destructive oxidation of the ben-zene ring (ozonolysis) with the involvement of the catalyst is explained by the fact that ozone under ca-talysis mainly reacts with a salt of manganese (II) and not with the substrate to form the active form of manganese Mn(IV) which has high substrate selectivity to alkylarenes, directs the oxidation of 4-bromoethylbenzene to the ethyl group. High selectivity of side chain oxidation is achieved only at ele-vated catalyst concentrations, which is largely due to the higher reaction rate of the substrate with ozone than with Mn(IV). The composition of the products of catalytic oxidation of 4-bromoethylbenzene depends on the temperature: at 293 K the reaction stops at the stage of formation of the corresponding ketone and acylated alcohol, increasing the temperature promotes further oxidation of 4-bromoacetophenone to 4-bromobenzoic acid, thus forming a mixture containing 4-bromoacetophenone (82.5 %), 1-(4-bromophenyl)ethanolacetate (4.2 %) and 4-bromo-benzoic acid (11.8 %). The research allowed to formulate general regularities of the reaction of catalytic oxidation of 4-bromomethylbenzene by ozone in acetic acid, to explain the role of the catalyst in the system and to propose a chemical scheme of oxidation corresponding to experimental data.

Phenomenological Variant of Quasi-Chemical Approximation in the Description of the Dimerisation of Adsorbate Molecules in a Multilayer Adsorption Phase on a Homogeneous Surface

This article is related thematically to two of our earlier publications, which demonstrated full equivalence of statistical and phenomenological methods in the description of physical gas adsorption on the surface of a solid body, and the fundamental possibility of analytical solution of adsorbate-adsorbate association problems in the entire multi-layer adsorption phase. The quasi-chemical scheme of secondary interactions leading to the formation of horizontal multimolecular adsorption complexes has been elaborated. A new adsorption equation was formulated taking into account the dimerisation of adsorbed molecules in the whole adsorption phase, as well as the influence of topography of the binding sites of adsorbent surfaces on the form of this solution.

Reduced chemical scheme for modelling warm to hot hydrogen-dominated atmospheres

Context. Three-dimensional models that account for chemistry are useful tools to predict the chemical composition of (exo)planet and brown dwarf atmospheres and interpret observations of future telescopes, such as James Webb Space Telescope (JWST) and Atmospheric Remote-sensing Infrared Exoplanet Large-survey (ARIEL). Recent Juno observations of the NH3 tropospheric distribution in Jupiter also indicate that 3D chemical modelling may be necessary to constrain the deep composition of the giant planets of the solar system. However, due to the high computational cost of chemistry calculations, 3D chemical modelling has so far been limited. Aims. Our goal is to develop a reduced chemical scheme from the full chemical scheme of Venot et al. 2012 (A&A, 546, A43) able to reproduce accurately the vertical profiles of the observable species (H2O, CH4, CO, CO2, NH3, and HCN). This reduced scheme should have a size compatible with three-dimensional models and be usable across a large parameter space (e.g. temperature, pressure, elemental abundance). The absence of C2H2 from our reduced chemical scheme prevents its use to study hot C-rich atmospheres. Methods. We used a mechanism-processing utility program designed for use with Chemkin-Pro to reduce a full detailed mechanism. The ANSYS© Chemkin-Pro Reaction Workbench allows the reduction of a reaction mechanism for a given list of target species and a specified level of accuracy. We took a warm giant exoplanet with solar abundances, GJ 436b, as a template to perform the scheme reduction. To assess the validity of our reduced scheme, we took the uncertainties on the reaction rates into account in Monte Carlo runs with the full scheme, and compared the resulting vertical profiles with the reduced scheme. We explored the range of validity of the reduced scheme even further by applying our new reduced scheme to GJ 436b’s atmosphere with different elemental abundances, to three other exoplanet atmospheres (GJ 1214b, HD 209458b, HD 189733b), a brown dwarf atmosphere (SD 1110), and to the troposphere of two giant planets of the solar system (Uranus and Neptune). Results. For all cases except one, the abundances predicted by the reduced scheme remain within the error bars of the model with the full scheme. Expectedly, we found important differences that cannot be neglected only for the C-rich hot atmosphere. The reduced chemical scheme allows more rapid runs than the full scheme from which it is derived (~30× faster). Conclusions. We have developed a reduced scheme containing 30 species and 181 reversible reactions. This scheme has a large range of validity and can be used to study all kinds of warm atmospheres, except hot C-rich ones that contain a high amount of C2H2. It can be used in 1D models, for fast computations, but also in 3D models for hot giant (exo)planet and brown dwarf atmospheres.

Atmospheric Chemistry of Gaseous Oxidized Mercury at a Coastal Site in Atlantic Canada

A chemistry box model containing a comprehensive suite of mercury (Hg) oxidation mechanisms involving O3, OH, H2O2, Br, BrO, NO2, HO2, and other oxidants was used to simulate the formation of gaseous oxidized mercury (GOM) and understand the chemical processes driving the observed trends in GOM at Kejimkujik, Nova Scotia, Canada. Simulations were conducted using chemical schemes with and without oxidation by O3 and OH. The major oxidants of Hg are O3 and OH (79%), H2O2 (10%), Br with second-stage HgBr oxidation by NO2 (7%), and BrO (3%) in simulations where all GEM oxidation reactions were considered simultaneously. In an alternative chemical scheme without gas-phase oxidation by O3 and OH, the dominant GOM species were HgBrNO2 (58%) and HgBrO (23.5%). Using this chemical scheme, the model reproduced the observed GOM at sub-ppqv Br2 mixing ratios. In the scheme with O3 and OH, the variability in GOM between seasons and between continental and marine air masses was mainly due to the variability in gaseous elemental Hg, O3, OH, and aerosol liquid water content (LWC). LWC governs the partitioning of GOM to the aerosol aqueous phase in the model. In the scheme without O3 and OH, the variability in GOM by season and airmass origin strongly depends on Br and BrO, suggesting that rigorous validation of modeled Br and BrO data are essential for improving the model predictions of GOM in coastal environments.