ReactionMechanismGenerator / ReactionMechanismGenerator/RMG-database

Biradicals 2S and 2T thermo and reactivity

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#19 2 comments 0 reactions 0 assignees View on GitHub

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Python
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Description

Noticed this when importing USC-Mech-ii.
RMG predicted some reactions that matched USC-Mech reactions, and created a H2CC species:

1 C 0  {2,D}
2 C 2T {1,D}

But the USC thermo is for the singlet:

1 C 0  {2,D}
2 C 2S {1,D}

Which is much more stable.
The DFT_QCI_Thermo database has both singlet and triplet in.
I am not sure what the reaction should make.

Probably we should have a state-crossing reaction, a bit like the 1,2-Birad_to_alkene family, that reacts H2CC(T) + M <=> C2CC(S) + M.

There may be other issues though - I'm not sure when RMG makes a 2T and when a 2S, nor am I sure if they are equally reactive in terms of matching nodes in reaction families.

See also:

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Research direction

Start by comparing issue #18 with the existing 1,2-Birad_to_alkene family and the singlet/triplet entries in the DFT_QCI_Thermo database. Trace when RMG creates 2T versus 2S species and how reaction-family node matching treats them. Done requires a decided and documented treatment of thermo, reactivity, and any state-crossing reaction.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
databases
Issue type
Bug
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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