Supplementary material to "Derivation of Atmospheric Reaction Mechanisms for Volatile Organic Compounds by the SAPRC Mechanism Generation System (MechGen)"

Abstract

A1. Chemical Mechanism Assignments and Estimates A1.1. Specification of ReactantsMechGen identifies the structure of organic reactants or radicals by specifying "groups" in the molecule, indicating the groups each is bonded to, and the type of bond. Groups are parts of molecules that are treated as units in the system and contain no more than one carbon or nitrogen, and also can contain zero to three hydrogen atoms and zero to three oxygen atoms. These group and molecule designations are used in the tables giving the parameters and assignments since these are how the parameters are assigned. The list of groups that can be used is given in Table A-1; illustrative examples are shown in Table A-2. Note also the following:• Neighboring groups in non-branched and non-cyclic structures are separated by either "-", "=", or "#" symbols depending on whether their bonds are single, double, or triple.• Branched structures are indicated using "( )" to show third or fourth groups bonded to groups with more than two neighbors. If the bond between the center group and the 3rd or 4th group is a double or triple bond it is indicated using a "=" or "#" after the "(", as shown for isoprene in Table A-2. This is similar to the treatment of branched structure using the SMILES notation (SMILES, 2022). Other examples are also shown in Table A-2.• Monocyclic structures are indicated using "*" symbols to indicate groups bonded to other groups using single bonds. The "*" can be before or after the group name, but the standard format is after the name. Bi-and polycyclic structures are indicated using "*1", "*2", etc. symbols to indicate groups that are bonded together, and should always be given after the group name but before any bond designation.• Aromatic structures can be created using "CH" and "C" groups with alternating single or double bonds as with other cyclic polyalkenes. However the standard designation, which reflects the fact that separate groups are used for aromatic carbons, is to designate carbons in aromatic rings using "aCH" or "aC" depending on whether it has a hydrogen or a third group bonded to it, with the aromatic bonds designated as if they were single bonds. See the example for toluene and naphthalene in Table A-2.• Allylic radicals can be created using carbon-centered radical groups and alkene groups to designate one of the resonance structures, and it does not matter which structure is used for this purpose. However the standard designation, which reflects the fact that separate groups are used for such radicals and the radical center is at more than one location, is to designate carbons where the radical center may be located as ".aCH2", "aCH[.]", or "aC[.]" and the other carbons in the allylic structure as if they are aromatic (i.e., alternating double and single bonds). This is only applicable for carbon-centered radicals with conjugated C=C double bonds. See, for example, the structures shown for methyl allyl radicals and the OH+benzene adduct in Table A-2.• Cis and trans isomerization about a double bond ar...