mcm_atmospheric — Master Chemical Mechanism and CRI mechanism of atmospheric chemistry (1999-2023)

Description

Networks of the chemical reactions of the Master Chemical Mechanism (MCM), a near-explicit mechanism of the gas-phase chemistry of the troposphere, which describes the degradation of 143 emitted volatile organic compounds (alkanes, alkenes, aromatics, isoprene, terpenes, oxygenated compounds, ...) and the inorganic chemistry of ozone, nitrogen oxides and sulfur, and is used in models of air quality. The reactions and their rate coefficients were derived by the MCM developers from measured kinetic data and from structure-activity relationships, following documented protocols.

The networks are directed and bipartite: nodes are chemical species and reactions, and an edge goes from each reactant to the reaction, and from the reaction to each of its products. A species that appears twice among the reactants (e.g. HO2 + HO2) or the products of a reaction gives parallel edges. Reactions without products (e.g. a sink of a species) only have edges from their reactants; the pseudo-species of photons (hv) and of unspecified products (PROD) of the KPP format are left out (photolysis reactions are marked as such).

There is one network for each version of the mechanism available from its website, from the files of the complete mechanism: v3.3.1 (exported in September 2023, KPP format), v3.2 (KPP format), v3.1 (FACSIMILE box model, 2005), v3.0 (FACSIMILE box model, 2003) and v2.0 (FACSIMILE box model, 1999). The box models of the older versions contain the reactions of the mechanism (with some reactions written as several lines with partial rate coefficients, which are kept as separate reactions, and reversible reactions, which are split into their forward and backward reactions), together with the setup of the model, which is ignored.

The Common Representative Intermediates mechanism (CRI), distributed from the same site, is a reduced mechanism derived from the MCM: the degradation of the emitted compounds is described with far fewer reactions and intermediate species, which are lumped into "representative intermediates" that conserve the ozone-forming potential of each compound (counted as its number of reactive bonds, C-C and C-H), and its parameters were optimized against the MCM in box-model simulations. CRI v2 was developed with MCM v3.1 as the reference. Its two versions available from the site are included, built in the same way, from the KPP files of the complete mechanism: cri_v2_1 (CRI v2.1, exported in June 2018: the reactions of CRI v2, with the revisions of rate coefficients of the transition from MCM v3.1 to v3.2) and cri_v2_2 (CRI v2.2, exported in September 2023: a substantially revised chemistry of isoprene, and the revisions of rate coefficients of the transition from MCM v3.2 to v3.3.1). The reduced variants of CRI with lumped emissions (R1-R5) are not among the files of the site and are not included.

Only v3.3.1 and cri_v2_2 have the properties of the species (structures, formulas and masses).

The networks have the following properties:

(Node) is_reaction: whether the node is a reaction (otherwise it is a species).
(Node) name: the name of the species in the MCM (e.g. O3, CH3O2, APINENE), or the equation of the reaction.
(Node) rate: the rate coefficient of the reaction, as an expression (in the syntax of the file: FORTRAN for KPP, FACSIMILE otherwise) of the temperature TEMP, of the concentrations of M, O2, N2, H2O, of named complex rate coefficients (e.g. KMT01, KRO2NO), of the sum of the peroxy radicals RO2, and, for photolysis, of the photolysis rates J(...) (empty for species).
(Node) is_photolysis: whether the reaction is a photolysis.
(Node) smiles, inchi, inchi_key, formula, mass (v3.3.1, cri_v2_2): the structure, formula and molar mass of the species (empty or NaN for reactions, and for the lumped species of CRI without a structure).
(Node) is_excited, is_peroxy_radical (v3.3.1, cri_v2_2): whether the species is an excited species, or a peroxy radical.

Tags

Chemical Unweighted Bipartite Multigraph Metadata

Added

2026-10-31

Citation

M. E. Jenkin, S. M. Saunders, M. J. Pilling, "The tropospheric degradation of volatile organic compounds: a protocol for mechanism development." Atmospheric Environment 31, 81-104 (1997) 10.1016/S1352-2310(96)00105-7 Sci-Hub
S. M. Saunders, M. E. Jenkin, R. G. Derwent, M. J. Pilling, "Protocol for the development of the Master Chemical Mechanism, MCM v3 (Part A): tropospheric degradation of non-aromatic volatile organic compounds." Atmospheric Chemistry and Physics 3, 161-180 (2003) 10.5194/acp-3-161-2003 Sci-Hub
M. E. Jenkin, S. M. Saunders, V. Wagner, M. J. Pilling, "Protocol for the development of the Master Chemical Mechanism, MCM v3 (Part B): tropospheric degradation of aromatic volatile organic compounds." Atmospheric Chemistry and Physics 3, 181-193 (2003) 10.5194/acp-3-181-2003 Sci-Hub
M. E. Jenkin, J. C. Young, A. R. Rickard, "The MCM v3.3.1 degradation scheme for isoprene." Atmospheric Chemistry and Physics 15, 11433-11459 (2015) 10.5194/acp-15-11433-2015 Sci-Hub
M. E. Jenkin, L. A. Watson, S. R. Utembe, D. E. Shallcross, "A Common Representative Intermediates (CRI) mechanism for VOC degradation. Part 1: Gas phase mechanism development." Atmospheric Environment 42, 7185-7195 (2008) 10.1016/j.atmosenv.2008.07.028 Sci-Hub
L. A. Watson, D. E. Shallcross, S. R. Utembe, M. E. Jenkin, "A Common Representative Intermediates (CRI) mechanism for VOC degradation. Part 2: Gas phase mechanism reduction." Atmospheric Environment 42, 7196-7204 (2008) 10.1016/j.atmosenv.2008.07.034 Sci-Hub
M. E. Jenkin, M. A. H. Khan, D. E. Shallcross, R. Bergström, D. Simpson, K. L. C. Murphy, A. R. Rickard, "The CRI v2.2 reduced degradation scheme for isoprene." Atmospheric Environment 212, 172-182 (2019) 10.1016/j.atmosenv.2019.05.055 Sci-Hub

Upstream URL OK

https://mcm.york.ac.uk/MCM
https://mcm.york.ac.uk/MCM/about/archive
https://mcm.york.ac.uk/CRI
https://mcm.york.ac.uk/CRI/about/archive

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$\oslash$	$S$	Kind	Mode	NPs	gt	GraphML	GML	csv
v3.3.1	22,530	55,455	2.46	61.40	48.76	6.58	-0.18	9	1.00	Directed	Bipartite	is_reaction name rate is_photolysis smiles inchi inchi_key formula mass is_excited is_peroxy_radical	726 KiB	1.0 MiB	1.0 MiB	925 KiB
v3.2	22,137	54,460	2.46	60.75	48.36	6.49	-0.18	9	1.00	Directed	Bipartite	is_reaction name rate is_photolysis	542 KiB	816 KiB	809 KiB	677 KiB
v3.1	19,420	46,015	2.37	52.66	42.75	6.54	-0.17	9	1.00	Directed	Bipartite	is_reaction name rate is_photolysis	473 KiB	703 KiB	690 KiB	578 KiB
v3.0	18,194	43,305	2.38	51.67	41.93	6.95	-0.18	9	1.00	Directed	Bipartite	is_reaction name rate is_photolysis	438 KiB	655 KiB	642 KiB	541 KiB
v2.0	14,255	36,447	2.56	50.28	41.76	9.21	-0.19	9	1.00	Directed	Bipartite	is_reaction name rate is_photolysis	348 KiB	519 KiB	514 KiB	431 KiB
cri_v2_2	1,700	4,860	2.86	21.94	20.24	9.28	-0.25	9	1.00	Directed	Bipartite	is_reaction name rate is_photolysis smiles inchi inchi_key formula mass is_excited is_peroxy_radical	52 KiB	71 KiB	70 KiB	63 KiB
cri_v2_1	1,621	4,539	2.80	20.85	19.42	9.28	-0.25	9	1.00	Directed	Bipartite	is_reaction name rate is_photolysis	44 KiB	61 KiB	60 KiB	52 KiB

Ridiculograms^*

^* These are automatically generated force-directed visualizations, and can be quite meaningless for networks both big and small. They should not be taken seriously as sources of scientific insight. See here for a discussion.