ReactionMechanismGenerator / ReactionMechanismGenerator/RMG-database

Singlet O=O vdW species in Surface_Adsorption_Abstraction_vdW

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Topic: Catalysis
Dominant language
Python
Stars
127
Forks
160
Avg merge
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Merged PRs (30d)
2

Description

As we discussed in #458, the gas phase O2 will be represented as [O][O], which has the following adjaceny list notation:

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

Since we don’t use the singlet O=O for the gas phase oxygen, do we want the vdW O2 to have this form in Surface_Adsorption_Abstraction_vdW family?

entry(
index = 11,
label = "O=O",
group =
"""
multiplicity [1]
1 *1 Xv u0 p0 c0
2 *2 O u0 p2 c0 {3,D}
3 *3 O u0 p2 c0 {2,D}
""",
kinetics = None,
)

We didn’t add the forbidden entry O=O in Surface_Adsorption_Bidentate family as well, and the following reaction will be created:
image

For consistency, should we keep all of them or remove the O=O entry

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by locating the Surface_Adsorption_Abstraction_vdW and Surface_Adsorption_Bidentate family definitions, then inspect the O=O entry at index 11 and the related forbidden-entry behavior. Compare these definitions with the [O][O] gas-phase representation and review the linked discussion and generated reaction example. Done means the project has a documented, consistent decision and the affected family entries reflect it.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
database
Issue type
Bug
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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