scholarly journals Improvement in Modeling of OH and HO2 Radical Concentrations during Toluene and Xylene Oxidation with RACM2 Using MCM/GECKO-A

Atmosphere ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 732
Author(s):  
Victor Lannuque ◽  
Barbara D’Anna ◽  
Florian Couvidat ◽  
Richard Valorso ◽  
Karine Sartelet
Keyword(s):  
Air Quality ◽  
Atmospheric Chemistry ◽  
Oxidation Mechanism ◽  
Chemical Mechanism ◽  
Flow Tube ◽  
Quality Models ◽  
Pollutant Formation ◽  
Master Chemical Mechanism ◽  
Kinetics Of ◽  
Ho2 Radical

Due to their major role in atmospheric chemistry and secondary pollutant formation such as ozone or secondary organic aerosols, an accurate representation of OH and HO2 (HOX) radicals in air quality models is essential. Air quality models use simplified mechanisms to represent atmospheric chemistry and interactions between HOX and organic compounds. In this work, HOX concentrations during the oxidation of toluene and xylene within the Regional Atmospheric Chemistry Mechanism (RACM2) are improved using a deterministic–near-explicit mechanism based on the Master Chemical Mechanism (MCM) and the generator of explicit chemistry and kinetics of organics in the atmosphere (GECKO-A). Flow tube toluene oxidation experiments are first simulated with RACM2 and MCM/GECKO-A. RACM2, which is a simplified mechanism, is then modified to better reproduce the HOX concentration evolution simulated by MCM/GECKO-A. In total, 12 reactions of the oxidation mechanism of toluene and xylene are updated, making OH simulated by RACM2 up to 70% more comparable to the comprehensive MCM/GECKO-A model for chamber oxidation simulations.

scholarly journals Mainz Isoprene Mechanism 2 (MIM2): an isoprene oxidation mechanism for regional and global atmospheric modelling

2008 ◽  
Vol 8 (4) ◽  
pp. 14033-14085 ◽  
Author(s):  
D. Taraborrelli ◽  
M. G. Lawrence ◽  
T. M. Butler ◽  
R. Sander ◽  
J. Lelieveld
Keyword(s):  
Atmospheric Chemistry ◽  
Oxidation Mechanism ◽  
Tropospheric Chemistry ◽  
Oxidation Products ◽  
Chemical Mechanism ◽  
Good Representation ◽  
Chemical Production ◽  
Global Models ◽  
Mixing Ratios ◽  
Isoprene Oxidation

Abstract. We present an oxidation mechanism of intermediate size for isoprene (2-methyl-1,3-butadiene) suitable for simulations in regional and global atmospheric chemistry models, which we call MIM2. It is a reduction of the corresponding detailed mechanism in the Master Chemical Mechanism (MCM v3.1) and intended as the second version of the well-established Mainz Isoprene Mechanism (MIM). Our aim is to improve the representation of tropospheric chemistry in regional and global models under all NOx regimes. We evaluate MIM2 and re-evaluate MIM through comparisons with MCM v3.1. We find that MIM and MIM2 compute similar O3, OH and isoprene mixing ratios. Unlike MIM, MIM2 produces small relative biases for NOx and organic nitrogen-containing species due to a good representation of the alkyl and peroxy acyl nitrates (RONO2 and RC(O)OONO2). Moreover, MIM2 computes only small relative biases with respect to hydrogen peroxide (H2O2), methyl peroxide (CH3OOH), methanol (CH3OH), formaldehyde (HCHO), peroxy acetyl nitrate (PAN), and formic and acetic acids (HCOOH and CH3C(O)OH), being always below ≈6% in all NOx scenarios studied. Most of the isoprene oxidation products are represented explicitly, including methyl vinyl ketone (MVK), methacrolein (MACR), hydroxyacetone and methyl glyoxal. MIM2 is mass-conserving with respect to carbon, including CO2 as well. Therefore, it is suitable for studies assessing carbon monoxide (CO) from biogenic sources, as well as for studies focused on the carbon cycle. Compared to MIM, MIM2 considers new species like acetaldehyde (CH3CHO), propene (CH2=CHCH3) and glyoxal (CHOCHO) with global chemical production rates for the year 2005 of 7.3, 9.5 and 33.8 Tg/yr, respectively. Our new mechanism is expected to substantially improve the results of atmospheric chemistry models by more accurately representing the interplay between atmospheric chemistry, transport and deposition, especially of nitrogen reservoir species. MIM2 allows regional and global models to easily incorporate new experimental results on the chemistry of organic species.

scholarly journals AtChem, an open source box-model for the Master Chemical Mechanism

2019 ◽  
Author(s):  
Roberto Sommariva ◽  
Sam Cox ◽  
Chris Martin ◽  
Kasia Borońska ◽  
Jenny Young ◽  
...  
Keyword(s):  
Open Source ◽  
Atmospheric Chemistry ◽  
Web Application ◽  
Box Model ◽  
Chemical Mechanism ◽  
Control Software ◽  
Sensitivity Studies ◽  
Master Chemical Mechanism ◽  
Field Campaigns ◽  
Set Up

Abstract. AtChem is an open source zero-dimensional box-model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism (MCM, http://mcm.york.ac.uk/). AtChem was initially developed within the EUROCHAMP project as a web application (AtChem-online, https://atchem.leeds.ac.uk/webapp/) for modelling environmental chamber experiments; it was recently upgraded and further developed into a standalone offline version (AtChem2) which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies. AtChem is installed, set up and configured using semi-automated scripts and simple text configuration files, making it easy to use even for non-experienced users. A key feature of AtChem is that it can easily be constrained to observational data which may have different timescales, thus retaining all the information contained in the observations. Implementation of a continuous integration workflow, coupled with a comprehensive suite of tests and version control software, makes the AtChem codebase robust, reliable and traceable. The AtChem2 code and documentation are available at https://github.com/AtChem/, under the open source MIT license.

scholarly journals OH and HO<sub>2</sub> radical chemistry in a midlatitude forest: Measurements and model comparisons

2019 ◽  
Author(s):  
Michelle L. Lew ◽  
Pamela S. Rickly ◽  
Brandon P. Bottorff ◽  
Sofia Sklaveniti ◽  
Thierry Léonardis ◽  
...  
Keyword(s):  
Atmospheric Chemistry ◽  
Global Climate ◽  
Oxidation Products ◽  
Chemical Mechanism ◽  
Ozone Production ◽  
Peroxy Radicals ◽  
Mixing Ratios ◽  
Photolysis Rates ◽  
Model Predictions ◽  
Ho2 Radical

Abstract. Reactions of the hydroxyl (OH) and peroxy radicals (HO2 and RO2) play a central role in the chemistry of the atmosphere. In addition to controlling the lifetimes of many trace gases important to issues of global climate change, OH radical reactions initiate the oxidation of volatile organic compounds (VOCs) which can lead to the production of ozone and secondary organic aerosols in the atmosphere. Previous measurements of these radicals in forest environments characterized by high mixing ratios of isoprene and low mixing ratios of nitrogen oxides (NOx) have shown serious discrepancies with modeled concentrations. These results bring into question our understanding of the atmospheric chemistry of isoprene and other biogenic VOCs under low NOx conditions. During the summer of 2015, OH and HO2 radical concentrations as well as total OH reactivity were measured using Laser-Induced Fluorescence - Fluorescence Assay by Gas Expansion (LIF-FAGE) techniques as part of the Indiana Radical, Reactivity and Ozone Production Intercomparison (IRRONIC). This campaign took place in a forested area near the Indiana University, Bloomington campus characterized by high mixing ratios of isoprene and low mixing ratios of NOx. Supporting measurements of photolysis rates, VOCs, NOx, and other species were used to constrain a zero-dimensional box model based on the Regional Atmospheric Chemistry Mechanism (RACM2) and the Master Chemical Mechanism (MCM). Using an OH chemical scavenger technique, the study revealed the presence of an interference with the LIF-FAGE measurements of OH that increased with both ambient concentrations of ozone and temperature. Subtraction of the interference resulted in measured OH concentrations that were in better agreement with model predictions, although the model still underestimated the measured concentrations, likely due to an underestimation of the concentration of NO at this site. Measurements of HO2 radical concentrations during the campaign included a fraction of isoprene-based peroxy radicals (HO2* = HO2 + αRO2) and were found to agree with model predictions. On average, the measured reactivity was consistent with that calculated from measured OH sinks to within 20 %, with modeled oxidation products accounting for the missing reactivity, although significant missing reactivity (approximately 40 % of the total measured reactivity) was observed on some days.

scholarly journals The community atmospheric chemistry box model CAABA/MECCA-4.0

2019 ◽  
Vol 12 (4) ◽  
pp. 1365-1385 ◽  
Author(s):  
Rolf Sander ◽  
Andreas Baumgaertner ◽  
David Cabrera-Perez ◽  
Franziska Frank ◽  
Sergey Gromov ◽  
...  
Keyword(s):  
Atmospheric Chemistry ◽  
Box Model ◽  
Chemical Mechanism ◽  
Chemical Mechanisms ◽  
Community Model ◽  
Volatile Organic ◽  
Master Chemical Mechanism ◽  
New Feature ◽  
User Friendly ◽  
Skeletal Mechanism

Abstract. We present version 4.0 of the atmospheric chemistry box model CAABA/MECCA that now includes a number of new features: (i) skeletal mechanism reduction, (ii) the Mainz Organic Mechanism (MOM) chemical mechanism for volatile organic compounds, (iii) an option to include reactions from the Master Chemical Mechanism (MCM) and other chemical mechanisms, (iv) updated isotope tagging, and (v) improved and new photolysis modules (JVAL, RADJIMT, DISSOC). Further, when MECCA is connected to a global model, the new feature of coexisting multiple chemistry mechanisms (PolyMECCA/CHEMGLUE) can be used. Additional changes have been implemented to make the code more user-friendly and to facilitate the analysis of the model results. Like earlier versions, CAABA/MECCA-4.0 is a community model published under the GNU General Public License.

Air quality modelling, simulation, and computational methods: a review

2013 ◽  
Vol 21 (3) ◽  
pp. 149-179 ◽  
Author(s):  
Mohanad El-Harbawi
Keyword(s):  
Air Quality ◽  
Computational Methods ◽  
Atmospheric Chemistry ◽  
Web Sites ◽  
Remote Sensing Data ◽  
Reference Source ◽  
Air Quality Modelling ◽  
Quality Models ◽  
Wide Range ◽  
Recent Developments

The objective of this paper is to provide a comprehensive theoretical review with regard to history, existing approaches, recent developments, major research, associated computational methods, and applications of air quality models. A wide range of topics is covered, focusing on sources of air pollution, primary and secondary pollutants, atmospheric chemistry, atmospheric chemical transport models, computer programs for dispersion modelling, online and offline air quality modelling, data assimilation, parallel computing, applications of geographic information system in air quality modelling, air quality index, as well as the use of satellite and remote sensing data in air quality modelling. Each of these elements is comprehensively discussed, covered, and reviewed with respect to various literature and methods related to air quality modelling and applications. Several major commercial and noncommercial dispersion packages are extensively reviewed and detailed advantages and limitations of their applications are highlighted. The paper includes several comparison summaries among various models used in air quality study. Furthermore, the paper provides useful web sites, where readers can obtain further information regarding air quality models and (or) software. Lastly, current generation of air quality models and future directions are also discussed. This paper may serve as a compendium for scientists who work in air quality modelling field. Some topics are generally treated; therefore, the paper may also be used as a reference source by many scientists working with air quality modelling.

scholarly journals Development of a chlorine chemistry module for the Master Chemical Mechanism

2015 ◽  
Vol 8 (6) ◽  
pp. 4823-4849
Author(s):  
L. K. Xue ◽  
S. M. Saunders ◽  
T. Wang ◽  
R. Gao ◽  
X. F. Wang ◽  
...  
Keyword(s):  
Atmospheric Chemistry ◽  
Southern China ◽  
Oxidative Capacity ◽  
Early Morning ◽  
Chemical Mechanism ◽  
Atmospheric Photochemistry ◽  
Nitryl Chloride ◽  
Chemistry Research ◽  
Master Chemical Mechanism ◽  
Chemistry Module

Abstract. The chlorine atom (Cl·) has a high potential to perturb atmospheric photochemistry by oxidizing volatile organic compounds (VOCs), but the exact role it plays in the polluted troposphere remains unclear. The Master Chemical Mechanism (MCM) is a near explicit mechanism that has been widely applied in the atmospheric chemistry research. While it addresses comprehensively the chemistry initiated by the OH, O3 and NO3 radicals, its representation of the Cl· chemistry is incomplete as it only considers the reactions for alkanes. In this paper, we develop a more comprehensive Cl· chemistry module that can be directly incorporated within the MCM framework. A suite of 199 chemical reactions describes the Cl·-initiated degradation of alkenes, aromatics, aldehydes, ketones, alcohols, and some organic acids and nitrates, along with the inorganic chemistry involving Cl· and its precursors. To demonstrate the potential influence of the new chemistry module, it was incorporated into a MCM box model to evaluate the impacts of nitryl chloride (ClNO2), a product of nocturnal halogen activation by nitrogen oxides (NOx), on the following-day's atmospheric photochemistry. With constraints of recent observations collected at a coastal site in Hong Kong, southern China, the modeling analyses suggest that the Cl· produced from ClNO2 photolysis may substantially enhance the atmospheric oxidative capacity, VOC oxidation, and O3 formation, particularly in the early morning period. The results demonstrate the critical need for photochemical models to include more fully chlorine chemistry in order to better understand the atmospheric photochemistry in polluted environments subject to intense emissions of NOx, VOCs and chlorine-containing constituents.

scholarly journals Chemical Mechanism Solvers in Air Quality Models

Atmosphere ◽  
2011 ◽  
Vol 2 (3) ◽  
pp. 510-532 ◽  
Author(s):  
Hong Zhang ◽  
John C. Linford ◽  
Adrian Sandu ◽  
Rolf Sander
Keyword(s):  
Air Quality ◽  
Chemical Mechanism ◽  
Quality Models

scholarly journals Global sea-surface iodide observations, 1967–2018

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Rosie J. Chance ◽  
Liselotte Tinel ◽  
Tomás Sherwen ◽  
Alex R. Baker ◽  
Thomas Bell ◽  
...  
Keyword(s):  
Air Quality ◽  
Observational Data ◽  
Atmospheric Chemistry ◽  
Tropospheric Ozone ◽  
Sea Surface ◽  
Digital Form ◽  
Quality Models ◽  
Surface Ocean ◽  
Data Points ◽  
Global Surface

AbstractThe marine iodine cycle has significant impacts on air quality and atmospheric chemistry. Specifically, the reaction of iodide with ozone in the top few micrometres of the surface ocean is an important sink for tropospheric ozone (a pollutant gas) and the dominant source of reactive iodine to the atmosphere. Sea surface iodide parameterisations are now being implemented in air quality models, but these are currently a major source of uncertainty. Relatively little observational data is available to estimate the global surface iodide concentrations, and this data has not hitherto been openly available in a collated, digital form. Here we present all available sea surface (<20 m depth) iodide observations. The dataset includes values digitised from published manuscripts, published and unpublished data supplied directly by the originators, and data obtained from repositories. It contains 1342 data points, and spans latitudes from 70°S to 68°N, representing all major basins. The data may be used to model sea surface iodide concentrations or as a reference for future observations.

scholarly journals Semantically enhanced provenance capture for chamber model development with a master chemical mechanism

2008 ◽  
Vol 367 (1890) ◽  
pp. 987-990 ◽  
Author(s):  
Chris J Martin ◽  
Mohammed H Haji ◽  
Peter M Dew ◽  
Michael J Pilling ◽  
Peter K Jimack
Keyword(s):  
Atmospheric Chemistry ◽  
Model Development ◽  
Computational Modelling ◽  
Chemical Mechanism ◽  
Scientific Communities ◽  
Chamber Model ◽  
Master Chemical Mechanism ◽  
Semantically Enhanced ◽  
Chemistry Community

The development and maintenance of benchmark databases within scientific communities is reliant on interactions with database users. We explore the role of semantically enhanced provenance for computational modelling processes that make use of one such database: the master chemical mechanism, a key resource within the atmospheric chemistry community.

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