The Master Chemical Mechanism |
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This page contains information on various aspects of the MCM, as follows
Prior to the present work, the Department for Environment, Food and Rural Affairs (DEFRA) 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 (Derwent et al., 1991)
During summertime, regional scale photochemical air pollution is a widespread phenomenon across much of north-west Europe and the UK. The production of elevated levels of ozone is of particular concern, since it is known to have adverse effects on human health, vegetation (e.g., crops) and materials. Established air quality standards for ozone are currently among the most widely exceeded of any pollutant in the UK, and the formulation of control strategies is therefore a major objective of environmental policy.
The main aim of the present collaborative project is to develop and apply predictive models to the formation of tropospheric ozone on a range of different geographical scales (i.e. global, regional and national). This is to underpin the formulation of policy with regard to the air quality and ambient levels of ozone in the United Kingdom. An essential part of the overall project is the MCM, as this mechanism underpins much of the current ozone modelling undertaken on the behalf of the DEFRA.
Here the work programme will focus primarily on the expansion and maintenance of the Master Chemical Mechanism (version 3: MCMv3) as a benchmark mechanism for chemical and photochemical processes in the troposphere. The following tasks will be performed:
The degradation schemes for aromatic hydrocarbons will be updated in line with new kinetic and mechanistic data, as they become available. The particular features of aromatic degradation which have the most influence on ozone formation will be identified by performing appropriate POCP sensitivity studies.
The representation of a number of gas-phase chemical processes will be updated in line with recently published kinetic and mechanistic data. This will include the following: (i) the reactions of OH with PAN species, (ii) the reactions of oxy radicals formed from degradation of esters and alkenes and (iii) the formation of excited oxy radicals from the reactions of some peroxy radicals with NO.
Photolysis rates of ozone and other inorganic and organic species will be updated in line with latest absorption cross-section and quantum yield data.
The feasibility of incorporating or improving the description of the formation of secondary sulphate and nitrate aerosol will be assessed, with the additional aim of improving the representation of heterogeneous chemical processes of particular importance (e.g. the reaction of N2O5 with water).
The updated MCM will be implemented into the Photochemical Trajectory Model (PTM), along with the latest amendments to the NAEI categorisation of sources (Digest of 1996 Emissions). A limited degree of validation of the updates to the MCM/PTM will be performed using a combination of ambient observational data and environmental chamber data.
The MCM website at Leeds University will be maintained and revised to include the updated MCM when completed.
Here one of the project objectives, the further development of the master chemical mechanism (MCMv3) for the gas phase tropospheric degradation of 124 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 fully tested against field and photochemical reactor data, although this is a subject of ongoing research. Initial studies of ozone formation in comparison with our previous chemical mechanism (Derwent et all., 1996) are in good agreement. More recent studies have also been carried out by evaluating the MCM against smog chamber and observational data (Jenkin et al. 1999). The overall results are very encouraging, and problem areas have been identified, which provide the impetus for further reviews and updates.
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.
Development and construction of a detailed chemical mechanism to describe the complete tropospheric oxidation of 124 volatile organic compounds (VOC) is presented. The VOC which are degraded in this mechanism were selected on the basis of available emissions data(Rudd 1995), and provide approximately 91% mass coverage of the emissions of uniquely identifiable chemical species. The majority of the degradation schemes have been constructed using the methodology described in an earlier publication(Jenkin et al., 1997). A brief review and update of the ideas behind the protocol document are given here. More recent developments in understanding aromatic oxidation have resulted in an extension of the protocol being used to update the aromatic schemes that were represented in MCMv2.0.
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 (MCMv3). The organic component of the MCMv3 contains in the region of 12600 reactions and 4500 chemical species.
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 this website MCM archive. 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 MCMv2.0 has been coded and fully integrated using Facsimile, within the UK photochemical trajectory model(30), to assess regional scale ozone formation across north west Europe and the British Isles. Photochemical Ozone Creation Potentials (POCP) were generated from the model results showing the relative importance of each VOC in ozone formation, on a mass emitted basis. The completed MCMv3.0 has now also been fully coded and integrated using Facsimile within the same model to provide comparisons with other work.
Details of the kinetic and mechanistic data used to construct the VOC degradation chemistry have been discussed in a separate publication (Jenkin et al., 1997). Briefly, the chemistry considered is summarised in figure 1.
Figure 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.
Figure 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 124 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. The earlier work for the development of MCMv1.0 was based on the customisation of commercially available PC oriented software, Accord(Synopsys) for Excel(Microsoft). 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(Curtis et al., 1987) 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.
Construction of new schemes to give a better description of the tropospheric degradation of aromatic compounds was begun, when Accord(Synopsys) for Access(Microsoft) was launched. Customisation of this new software enabled the entire MCM to be stored and constructed within a chemical database environment.
The initial MCM work could not have been developed in the database system, as it was not available on the market, and also it could initially only handle species and not reactions. The version utilized handles reactions, so the entire MCM was converted into the database system, which is capable of further scheme expansion. Figure 3 shows MCM database system in form view. It contains all the information that was contained in the spreadsheet system, but here the chemistry window displays a reaction, and there is also the REACTION smiles string below.
Figure 3
This has many advantages over the spreadsheet, in that the entire MCM is a single database. In the spreadsheet system it was not possible to have a complete MCM file. The mechanisms were constructed with separate spreadsheet files of the individual VOC mechanisms. The MCM database with records from 1 - 12600, can be searched and browsed with the standard database facilities, and there is also the enhancement of Chemical structure searching. The major advantage though is that it is capable of further expansion
The data base can export information in various formats which results in the generation of the complete master mechanism (MCM) text file. This file describing the tropospheric degradation of the 124 VOC and associated inorganic chemistry contains in excess of 12600 reactions and 4500 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.
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 et al. 1994, 1990, 1991, 2000, Roberts 1990, Wayne et al, 1991., Lightfoot et al. 1992, Carter and Atkinson 1985, Atkinson and Carter 1992, DeMore et al. 1997, Calvert et al. 2000, 2000a). 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. 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. 1992 and Wallington et al.. The present protocol aims to take into consideration work available in the open literature up to the mid-2001, and some further studies known by the authors, which were under review at that time.
New work since the publication of the original protocol paper (Jenkin 1997) has been taken into consideration in the production of MCMv3. The revised protocol is detailed in reference (Saunders et al. 2003a)
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:
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:
Further details of the mechanism protocol for non-aromatic compounds can be found in references (Jenkin 1997), (Saunders 2003a). A summary of the chemistry considered is given in Fig.1.
The degradation chemistry of aromatic VOC remains an area of particular uncertainty, and the schemes within MCMv3.1 have been substantially updated from MCMv3.0. The schemes for benzene, toluene, p-xylene and 1,3,5-trimethylbenzene have been tested against environmental chamber data as part of the EU-funded programme, Effects of oxidation of aromatic compounds in the troposphere (EXACT). In order to provide a detailed description of tropospheric degradation, the aromatic oxidation mechanisms have been developed aiming to fulfill a number of criteria:
(a) represent the complete degradation
(b) give a reasonable description of known organic product formation
(c) give a description of ozone formation which is consistent with hydrocarbon/NOX chamber observations
(d) include speciated organic products which are known to contribute to secondary organic aerosol (SOA) formation and growth.
Some of the features are illustrated in the schematic shown below for toluene, which emphasizes the multi-step nature of the oxidation mechanisms, and the role aromatic hydrocarbons can have in the generation of ozone and SOA.
Although a major objective of the mechanism development is to provide an acceptable description of ozone formation, the schemes also include the formation of species such as furanones, furandiones, quinones and nitrophenols which have been detected as notable constituents of SOA.(Forstner et al. 1997)
A reasonable amount of quantitative information on first generation products is now available, at least for the oxidation of selected aromatics. (e.g. Kwok et al. 1997 Klotz et al. 1998, 1998a, Ghigo, Bohm et al. 1999, Moschonas et al. 1999 Smith et al. 1999, Berndt et al. 1999, Barnes et al. 2000)
The primary oxidation steps include:
(i) minor routes to aromatic aldehydes (except in the case of benzene)
(ii) routes to phenolic compounds. Note that further oxidation of these compounds can lead to the formation of para-quinones which were previously assumed to be formed in a separate route
(iii) routes to the formation of a-dicarbonyls (and co-products)
In the majority of cases for which information is available, these routes do not provide a complete carbon balance, and additional routes need to be invoked, based on other detected (but unquantified) products.
Figure 4
Similar templates have been used for all the aromatic compounds, currently incorporated into the MCMv3, accounting for all the major products which have been determined experimentally.
The protocol for MCMv3.0 aims to take into consideration work available in the open literature up to mid-2001, and details have been published(Jenkin et al. 2003b)
Unless otherwise stated the treatment of intermediates, both radical and stable, follows the protocol developed previously ( Jenkin et al. 1997>, Saunders et al. 2003a).
The EU-funded programme, Effects of oXidation of Aromatic Compounds in the Troposphere (EXACT), placed a great deal of emphasis on trying to understand aromatic tropospheric degradation pathways. MCMv3.1 builds on the development of MCMv3.0, it incorporates the results of the EXACT project and represents our current understanding of aromatic degradation. Further details of these updates are being prepared for publication. However, EXACT has also shown that uncertainties still remain in unravelling tropospheric aromatic oxidation mechanisms and further developments may be possible in the future
