Tropospheric Chemistry Modelling



The new MCM version 2.0 can now be found on the CAST site.

The Atmospheric research group in the Department of Chemistry, consists of several groups working in closely related areas, studying a wide variety of topics of relevance to atmospheric processes. The Tropospheric Chemistry Modeling group is involved with all aspects of model construction and application. Part of this work has been a collaborative project, funded by the Department of the Environment, aimed at IMPROVING CURRENT MODELS AND APPLICATION TO POLICY ISSUES.

Overview of Contents

Personnel involved
Project description
The MCM - Master Chemical Mechanism
Other related work

The Personnel Involved

School of Chemistry, University of Leeds
Prof. Mike Pilling Dr. Sam Saunders

AEA Technology, National Environmental and Technology Centre, Culham
Dr. Mike Jenkin

Atmospheric Processes Research Branch, Meteorological Office, Bracknell
Dr. Dick Derwent

Project description

Prior to the present work, the Department of the Environment (DoE) had supported the development of explicit chemical mechanisms which describe the individual roles played by each volatile organic compound (VOC), for incorporation in photochemical trajectory models. These mechanisms are now used within EMEP and elsewhere in Norway, Sweden, France and Switzerland, and have been used to quantify the potential that each VOC exhibits to from photochemical ozone, through the development of the Photochemical Ozone Creation Potential (POCP) concept (1)

The main aim of the present collaborative project has been to improve and extend the DoE photochemical Trajectory Model, and thereby provide a more complex and sophisticated policy tool for the description of the roles of VOC and NOx in regional scale photo-oxidant formation over Europe. To achieve this several specific objectives for a 3 year work program were identified :

Here one of the project objectives, the development of a master chemical mechanism (MCM) for the gas phase tropospheric degradation of 120 volatile organic compounds is presented.

The mechanism aims to provide a RESEARCH TOOL for investigating not only the production of ozone but also for application in areas where detailed chemistry is required, eg. the generation of intermediates (eg. multifunctional carbonyls, hydroperoxides and nitrates) for which field data are becoming available and how the generation of these products is influenced by newly identified or postulated chemical pathways or redetermined kinetic parameters. The mechanism is flexible and can accommodate a full range of VOC:NOx ratios. While the mechanism is based on available laboratory data, it has not been tested against field and photochemical reactor data, although this is a subject of current research. Preliminary studies of ozone formation in comparison with our previous chemical mechanism (4) are in good agreement.

The MAIN INTENTION of this web site is to provide a flexible, easily utilised platform for the MCM that is readily accessed by the whole research community, and to promote its collaborative development and validation.

To access the mechanism click here for a description on the VOC LISTING.

Introduction to the MCM

Development and construction of a detailed chemical mechanism to describe the complete tropospheric oxidation of 120 volatile organic compounds (VOC) is presented. The VOC which are degraded in this mechanism were selected on the basis of available emissions data(2), and provide approximately 97% mass coverage of the emissions of uniquely identifiable chemical species. The degradation schemes have been constructed using the methodology described in an earlier publication(3). A brief review of the ideas behind the protocol document are given here
The degradation schemes are currently being used to provide an up to date mechanism for the production of secondary oxidants, for use in a model of the boundary layer over Europe. The schemes constructed using this protocol are applicable, however, to a wide range of ambient conditions, and may be employed in models of urban, rural or remote tropospheric environments, or for the simulation of secondary pollutant formation for a range of NOx or VOC emission scenarios. These schemes are believed to be particularly appropriate for comparative assessments of the formation of oxidants, such as ozone, from the degradation of organic compounds.
Compilation of the individual VOC degradation schemes has produced the Master Chemical Mechanism (MCM). The organic component of the MCM contains in the region of 7000 reactions and 2500 chemical species. With the exception of 18 aromatic compounds, the chemistry was constructed using the protocol described previously(3). The aromatic chemistry was based on that used in previous work(1,4), but was extended to include the reactions of peroxy radicals with HO2 and NO3, and the permutation reactions of the peroxy radicals. Although there are currently many gaps and uncertainties in the details of the atmospheric degradation mechanisms of aromatic compounds(5), there are several groups active in this field of research(6,7), and new data are constantly emerging.
The difficulties associated with ensuring that there was no species or nomenclature duplication within the compiled mechanism, led to the development of computerised mechanism construction. Details of the format and operation of the computerised system are described herein. Also, due to the large size of the MCM, it is not possible to provide the listing in hard copy. Full facsimile coding is available, together with associated mechanism and species files via e-mail and the Web. The concepts behind the methodology of the mechanism development and construction are such that as new data becomes available the MCM can be updated, utilising the computer aided construction format.
The completed MCM has been coded and fully integrated using Facsimile, within the UK photochemical trajectory model(4), to assess regional scale ozone formation across north west Europe and the British Isles. A Photochemical Ozone Creation Potential (POCP) index is being generated from the model results showing the relative importance of each VOC in ozone formation, on a mass emitted basis.

Construction of the Master Chemical Mechanism (MCM)

Details of the kinetic and mechanistic data used to construct the VOC degradation chemistry have been discussed in a separate publication (3). Briefly, the chemistry considered is summarised in Fig.1. The degradation is initiated by reaction with OH and, where appropriate, direct photolysis and the reactions with O3 and NO3. The types of radical generated following initiation processes include peroxy (RO2), oxy (RO) and excited and stabilised Criegee (R'R"COO) species, which each have a number of possible reactions which may be competitive under tropospheric conditions (see Fig.1). The complex initiation and radical chemistry leads to the generation of many different products. Some are species which themselves have primary emissions, such as simple alcohols, aldehydes and ketones; others include complex (multifunctional) carbonyls, nitrates (RONO2), peroxy nitrates (RC(=O)OONO2), hydroperoxides (ROOH), percarboxylic acids (RC(=O)OOH) and carboxylic acids (RC(=O)OH). To describe the complete tropospheric degradation of the VOC, these products are in turn degraded resulting, eventually in the final degradation products CO2 and H2O.
An example of the degradation chemistry constructed using the protocol (3), is displayed schematically in Fig.2. This shows a large part of the chemistry which makes up the mechanism for the partial degradation of butane. The chemistry along a given degradation pathway is developed until the VOC, in this case butane, is broken down into CO2, CO or an organic product (or radical) which is treated independently elsewhere in the MCM. Hence in this case the first generation carbonyl products, butanone (CH3C(=O)C2H5) and n-butanal (n-C3H7CHO) are degraded no further in this VOC scheme, as they are primary emitted compounds which are treated independently. The schemes expand very rapidly when compiling the complete oxidation of the VOC and all products that are generated. For butane, as a single primary VOC, the full degradation scheme consists of 510 reactions and 186 species, of which 20 are themselves primary emitted VOC.
The large number of reactions and species needed to construct the degradation chemistry of all 120 VOC led to inherent problems in trying to ensure no species duplication in either nomenclature or chemical structure. To overcome these difficulties a computerised mechanism generation system was developed, based on the customisation of commercially available PC oriented software, Accord(8) for Excel(9). Excel is a well known spreadsheet, that forms part of the integrated software package, Microsoft Office for Windows, and Accord is an add-on to this system, which transforms Excel into a chemical spreadsheet, with the addition of an extended range of functions on a chemistry tool bar. This allows identifiable chemical structures to be stored within the spreadsheet cells. Facilities supported by the software enable chemical structure and nomenclature searches to be performed. A macro has been set up for the specific task of mechanism construction, in which both the species structure and nomenclature are cross-referenced automatically against a cumulative reference species file. The nomenclature could have taken various formats, such as a linear representation of the carbon chain and associated side branches, or the scientific name of the species. However, in general for chemical mechanisms to be implemented in computer modelling studies, the input file usually has some restrictions on format. In this case for incorporation into the UK photochemical trajectory model, which uses Facsimile(10) as the integrator, the maximum field size for the separate species names was 10 alphanumeric characters, which also could not begin with a numeric character. Hence the species file was constructed to contain the structural information, and associated species code names, which observed the Facsimile format restrictions.
Using butanal as an example, the individual VOC degradation schemes are constructed in the following manner. Each primary VOC scheme begins by opening a new spreadsheet file. This overlays a background file EXTSPEC, the cumulative reference species file. The spreadsheet cells contain data relevant to the species, their species code name and chemical structure. These are entered either by using the SMILES(11) input notation of the input chemistry function on the chemistry tool bar, or by using a chemical drawing package, such as ChemDraw(12), and cutting and pasting the structure into the spreadsheet cell. The stored chemical structures can be readily displayed using the draw structure icon, Fig.3
As species are introduced onto the mechanism worksheet, running the macro, allows that species to be cross-referenced with species that are already present in that, or any other mechanism, via the construction and update of the background reference file. The macro performs an interrogation of the background species file, and searches for both chemical structure and nomenclature. If the species is already present on the species file, the assigned code name is copied onto the mechanism worksheet. If the species is unknown it is appended to the bottom of the species file with a unique code name, and used in all subsequent cross-checking. The mechanism files generated in this system are of a very specific Accord.xls format, which contain all the information required to give the full chemical representation of the species. For incorporation into the photochemical trajectory model only the reactions represented by species code names and the associated rate data are required in standard ASCII text format. These files are produced using cut and paste facilities, to copy the appropriate data from the Accord.xls worksheet to a text editor file.
Combination of all the VOC mechanism files results in the generation of the complete master mechanism (MCM) text file. This file describing the tropospheric degradation of the 120 VOC and associated inorganic chemistry contains in excess of 7000 reactions and 2500 chemical species. It is readily transportable via electronic mail, copies of which can be obtained by contacting sandras@chem.leeds.ac.uk. Files can also be downloaded from this web site. Periodic reviews and updates of the MCM will also be given in bulletins on this web page.

Bibliography

[1]	R.G. Derwent and M.E. Jenkin - Hydrocarbons and the long range transport of ozone and PAN across Europe. Atmos. Environ. 25A p1661 (1991)
[2]	H.J. Rudd - Emissions of volatile organic compounds from stationary sources in the United Kingdom : speciation. Report AEA/CS/16419033/REMA-029 (1995)
[3]	M.E. Jenkin, S.M. Saunders and M.J. Pilling - The tropospheric degradation of volatile organic compounds : a protocol for mechanism development. Atmos. Environ. 31 p31 (1997)
[4]	R.G. Derwent, M.E. Jenkin and S.M. Saunders - Photochemical ozone creation potentials for a large number of reactive hydrocarbons under European conditions. Atmos. Environ. 30 p189 (1996)
[5]	R. Atkinson - Kinetics and mechanisms of the gas phase reactions of the hydroxyl radical with organic compounds. J. Phys. Chem. Ref. Data Monograph 2 (1994)
[6]	G. Le Bras (coordinator) - EUROTRAC Annual Report, Part 8 LACTOZ (1993)
[7]	H. Jeffries, Y. Jianzhen and L. Bartolotti - Theoretical and analytical advances in understanding aromatic atmospheric oxidation mechanisms. 210th ACS National Meeting. Paper Number PHYS-15. Chicago, Ill, August 20, (1995)
[8]	Synopsys Scientific Systems Ltd. 175 Woodhouse lane, Leeds LS2 3AR, UK.
[9]	Microsoft Corporation, USA
[10]	A.R. Curtis and W.P. Sweetenham - FACSIMILE release H user's manual. AERE report R11771 (HMSO), London, (1987)
[11]	D. Weininger - SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28 p31 (1988)
[12]	Cambridge Scientific Computing, Inc. - 875 Massachusetts avenue, Cambridge, MA 02139, USA.
[13]	R. Atkinson - Gas-phase tropospheric chemistry or organic compounds : a review. Atmospheric Environment, 24A p1-41(1990).
[14]	J.M. Roberts - The atmospheric chemistry of organic nitrates. Atmospheric Environment, 24A p243-287 (1990).
[15]	R.P Wayne, I.Barnes, P.Biggs, J.P.Burrows, C.E. Canos-Mas, J.Hjorth, G. LeBras, G.K. Moortgat, D.Perner, G. Poulet, G.Restelli and H.Sidebottom - The nitrate radical: physics, chemistry and the atmosphere. Atmospheric Environment, 25A p1-206 (1991).
[16]	P.D. Lightfoot, R.A. Cox, J.N. Crowley, M.Destriau, G.D. Hayman, M.E. Jenkin, G.K. Moortgat and F. Zabel - Organic peroxy radicals : kinetics, spectroscopy and tropospheric chemistry. Atmospheric Environment, 26A p1805-1964 (1992).
[17]	W.P.L. Carter and R. Atkinson - Atmospheric chemistry of alkanes. J. Atmos. Chem., 3 p377-405 (1985).
[18]	R. Atkinson - Kinetics and mechanisms of the gas-phase reactions of the nitrate radical with organic compounds. J. Phys. Chem. Ref. Data, 20, p459 (1991).
[19]	R. Atkinson and W.P.L. Carter - Reactions of alkoxy radicals under atmospheric conditions. The relative importance of decomposition versus reaction with O2. J. Atmos. Chem., 13 p195 (1991).
[20]	T.J. Wallington, P. Dagaut and M.J. Kurylo - Ultra-violet absorption cross sections and reaction kinetics and mechanisms for peroxy radicals in the gas phase. Chem. Rev., 92, p667-710 (1992).

Project Objectives

To improve the treatment of atmospheric chemistry in the photochemical trajectory model by updating the simple C, O, H, N and S chemistry, the existing treatment of organic compounds and improving the calculations of the photolysis rates.
To expand the treatment of VOC's to address approximately 120 for which both atmospheric emissions and degradation pathways can be postulated. To review present and new degradation schemes.
To generate consistent and well defined POCP values for the VOCs and to comment on their policy significance. To validate the model against emission inventories for the UK and Europe.
To improve the representation of meteorology and boundary layer processes in the model. To consider the treatment of aerosol formation and visibility.
To evaluate the remaining uncertainties in the evaluation of policy strategies for the control of photochemical ozone in Europe. To evaluate the use of different emission inventory databases and emission control policies and end points. To develop a user interface so that the model can be utilised in a policy environment.
To consider the problem of model validation, including the role of both laboratory studies and field measurements.

Brief Protocol Review

In recent years, the availability of kinetic and mechanistic data relevant to the oxidation of VOCs has increased significantly, and various aspects of the tropospheric chemistry of organic compounds have been reviewed extensively (eg. Atkinson [5,13], Roberts [14], Wayne et al.[15], Lightfoot et al.[16]). In this work, the available information was used to define a series of rules which can be used to construct detailed degradation schemes for a range of organic compounds, for use in numerical models. These rules are intended to apply to the treatment of many hydrocarbons and oxygenated and chlorinated VOCs, with the notable exception of aromatic species, for which there are still major uncertainties in our understanding of the detailed chemistry. The present work draws heavily on previous reviews and evaluations, in particular the numerous, excellent publications of Atkinson and co-workers (eg. Carter and Atkinson [17], Atkinson [5,13,18], Atkinson and Carter [19]). Where necessary, existing recommendations are adapted, or new rules are defined, to reflect recent improvements in the database, particularly with regard to the treatment of peroxy radical (RO2) reactions for which there have been major advances, even since the comparatively recent reviews of Lightfoot et al. [16] and Wallington et al. [20]. The present protocol aims to take into consideration work available in the open literature up to the end of 1994, and some further studies known by the authors, which were under review at that time.
The major disadvantage of explicit chemical mechanisms, is the very large number of reactions potentially generated, if a series of rules is rigorously applied. A practical protocol for mechanism development must therefore aim to limit the number of reactions in a degradation scheme, whilst maintaining the essential features of the chemistry and minimising significant a priori assumptions. In the present work, a degree of strategic simplification is applied which substantially reduces the total number of reactions describing the degradation of a given VOC.
The protocol is designed to allow the construction of comprehensive and consistent degradation schemes for a range of VOCs. It is divided into ten subsections, as follows:
1. OH radical initiation reactions.
2. O3 initiation reactions.
3. NO3 radical initiation reactions.
4. Initiation by photolysis.
5. Reactions of organic radicals.
6. Reactions of peroxy radical intermediates.
7. Reactions of Criegee biradical intermediates.
8. Reactions of oxy radical intermediates.
9. Removal of chlorine atoms.
10. Reactions of degradation products.
In sections 1-3, the initiation reactions of OH radicals with organic compounds are considered, and guidelines are established to indicate for which compounds O3 and NO3 initiated chemistry is also likely to be important, and should also be treated. Photolysis reactions, which are significant for some classes of VOC, are identified in section 4 and photolysis rates are assigned to a series of generic reactions. In sections 5-9, the reactions of the reactive intermediates generated as a result of the initiation chemistry are identified, and various generic parameters and criteria are summarised. In the final subsection, the further degradation of first, and subsequent generation products is discussed.
The rules are also designed to lead to some strategic simplification in the degradation schemes generated. This is generally achieved in three ways:
1. The number of product channels resulting from the attack of OH on many VOCs is limited by disregarding those of low probability.
2. The many "permutation reactions" of a given peroxy radical are represented by a single parameterised reaction.
3. The degradation chemistry of the products is significantly simplified in many cases, particularly for the "side products" such as organic nitrates, peroxy nitrates, hydroperoxides, percarboxylic acids, carboxylic acids and alcohols, since these are usually comparatively minor.

Further details of the mechanism protocol can be found in reference [3]. A summary of the chemistry considered is given in Fig.1.

VOC LISTING

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IMPORTANT NOTES - Please read carefully before attempting to explore the MCM

The MCM can be explored or downloaded in several ways :-
Click here for access to the complete MCM archive files.
OR BROWSE the MCM pages for species/compounds of interest
The complete MCM comprises all the linked segments and should be considered in its entirety. The section displayed under a VOC heading DOES NOT give a full mechanism for that VOC. It simply provides a pointer to locate the chemistry associated with a specific VOC. Species not degraded in that section can be located elsewhere in the MCM. For example, the degradation of butane generates n-butanal and the chemistry associated with n-butanal is located on a separate page accessed from the VOC listing under the aldehyde grouping.
The species file gives a complete listing of the code names used in the MCM, together with a linear representation of the associated chemical structure using the SMILES notation. The Smiles string is quite straight forward to interpret, and at present is the only definition available to UNIX based users. However for PC based users, the SMILES string can be interpreted by spawning an external VIEWER using the Chemical MIME data exchange mechanism, which will display the chemical structure on screen. Click here for details on setting up and using the ACCORD Internet Chemistry Viewer if required.
Interpretation of the coded species names is possible by exploring the species file, which is also accessible from specific VOC mechanism pages.
Due to the many gaps and uncertainties in the aromatic chemistry, the level of detail that has been incorporated at this stage does not mirror that of all the other VOC. This is a major objective of the ongoing to work, to provide an up-to-date detailed description of troposheric aromatic degradation.
Definition of generalised rate parameters used in the MCM are given in this summary table
To begin browsing the MCM, first select the compound class of interest from this classification table.

**VOC classification in the MCM**
Inorganic section
Alkanes	22
Alkenes	15
Dialkenes	2
Alkynes	1
Aromatics	18
Aldehydes	6
Ketones	10
Alcohols and Glycols	17
Ethers and Glycol ethers	10
Esters	8
Organic acids	3
Chloro- and Hydrochlorocarbons	8
Cl atom + Alkane reactions

INORGANIC CHEMISTRY

ORGANIC CHEMISTRY

ALKANES

CL ATOM + ALKANE REACTIONS

CL ATOM + ALKANE REACTIONS

ALKENES

DIALKENES

ALKYNES

ETHYNE (ACETYLENE)

ALDEHYDES

KETONES

ALCOHOLS AND GLYCOLS

ETHERS AND GLYCOL ETHERS

ESTERS

ORGANIC ACIDS

CHLORO AND HYDROCHLOROCARBONS

AROMATICS

Figure 1: Summary of chemistry condidered in the mechanism protocol..

Figure 2: Schematic representation of the degradation of butane..

Figure 3: Display of butanal mechanism file showing chemical structure..

Related work

Information on some other projects related to atmospheric chemistry, carried out in Leeds can be found here :-

Atmospheric chemistry at Leeds
Mobile Atmospheric Chemistry Unit

OR further afield at :-

National Air Quality Information Archive
US Environmental Protection Agency (EPA)

Enquiries

For queries about the Chemistry, contact Nicola Carslaw
(nicolas@chem.leeds.ac.uk)
Tel : +44(0) 113 233 6486
For technical issues concerning the Web Site, contact Ben Whitaker
(benw@chem.leeds.ac.uk)
Last Modified on 6.4.98