10. Species Representation

Species objects in RMG contain a variety of attributes, including user given names, thermochemistry, as well as structural isomers. See the rmgpy.species.Species class documentation for more information.

RMG considers each species to be unique, and comprised of a set of molecular structural isomers, including resonance isomers. RMG uses the list of resonance isomers to compare whether two species are the same. Each molecular structure is stored in RMG using graph representations, using vertices and edges, where the vertices are the atoms and the edges are the bonds. This form of representation is known as an adjacency list. For more information on adjacency lists, see the Adjacency Lists page.

Species objects in the input file can also be constructed using other common representations such as SMILES, SMARTS, and InChIs. The following can all be used to represent the methane species:

species(
    label='CH4',
    reactive=True,
    structure=SMILES("C"),
)

Replacing the structure with any of the following representations will also produce the same species:

structure=adjacencyList("
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
"),

structure=SMARTS("[CH4]"),

structure=SMILES("C"),

structure=InChI("InChI=1S/CH4/h1H4"),

To quickly generate any adjacency list, or to generate an adjacency list from other types of molecular representations such as SMILES, InChI, or even common species names, use the Molecule Search tool found here: http://rmg.mit.edu/molecule_search

10.1. Representing Oxygen

Special care should be taken when constructing a mechanism that involves molecular oxygen. The ground electronic state of molecular oxygen, \(^3\Sigma^-_g\), does not contain a double bond, but instead a single bond and two lone electrons. In RMG’s adjaceny list notation the ground state of oxygen is represented as

1 O u1 p2 {2,S}
2 O u1 p2 {1,S}

You should use the above adjacency list to represent molecular oxygen in your condition files, seed mechanisms, etc. The triplet form is 22 kcal/mol more stable than the first singlet excited state, \(^1\Delta_g\), which does contain a double bond. The adjacency list for singlet oxygen is

1 O u0 p2 {2,D}
2 O u0 p2 {1,D}

Selecting the correct structure for oxygen is important, as the reactions generated from a double bond are significantly different than those generated from a radical or diradical. For example, the reaction

\[\mathrm{CH_4} + \mathrm{O_2} \rightarrow \mathrm{CH_3} + \mathrm{HO_2}\]

would occur for both triplet and singlet oxygen, but in entirely different families. For triplet oxygen the above represents a hydrogen abstraction, while for singlet oxygen it represents the reverse of a disproportionation reaction.

The RMG databases have been modified to make all of the oxygen-related chemistry that was present in RMG databases consistent with the single-bonded biradical representation.

Conversion between triplet and singlet forms is possible through the primary reaction library OxygenSingTrip; the reactions involved are very slow, however, and are likely to be absent from any mechanisms generated. At this point, no other reactions of singlet oxygen have been included in RMG.

In order to allow the singlet form of O2 to be used in RMG, please allow it explicitly by setting allowSingletO2 to True in the generateSpeciesConstraints section of the RMG input file.

generatedSpeciesConstraints(
    allowSingletO2 = True,
)