ReactionMechanismGenerator / ReactionMechanismGenerator/RMG-database
Biradicals 2S and 2T thermo and reactivity
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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:
- issue #18.
- http://dx.doi.org/10.1063/1.1456508
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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