Representing oxygenΒΆ
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) O2 0.1 (mol/cm3)
1 O 1 {2,S}
2 O 1 {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) O2 0.1 (mol/cm3)
1 O 0 {2,D}
2 O 0 {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.
Previous versions of RMG databases were ambiguous as to the treatment of oxygen, with both ChemGraphs above representing ground-state oxygen. The database provided with RMG 3.2 has 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.
