ReactionMechanismGenerator / ReactionMechanismGenerator/RMG-database

Group Additivity Double Counting - O2s-O2s(Cds-O2d) and O2s-OsH

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Complexity: Low Topic: Thermo
Dominant language
Python
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Merged PRs (30d)
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Description

Looks like we may be double counting with O2s-O2s(Cds-O2d) and O2s-OsH groups:

example with O=COO
https://rmg.mit.edu/database/thermo/molecule/1%20O%20u0%20p2%20c0%20%7B2,D%7D%0A2%20C%20u0%20p0%20c0%20%7B1,D%7D%20%7B3,S%7D%20%7B5,S%7D%0A3%20O%20u0%20p2%20c0%20%7B2,S%7D%20%7B4,S%7D%0A4%20O%20u0%20p2%20c0%20%7B3,S%7D%20%7B6,S%7D%0A5%20H%20u0%20p0%20c0%20%7B2,S%7D%0A6%20H%20u0%20p0%20c0%20%7B4,S%7D%0A

example with O=C(C)OO
https://rmg.mit.edu/database/thermo/molecule/1%20O%20u0%20p2%20c0%20%7B2,D%7D%0A2%20C%20u0%20p0%20c0%20%7B1,D%7D%20%7B3,S%7D%20%7B4,S%7D%0A3%20C%20u0%20p0%20c0%20%7B2,S%7D%20%7B6,S%7D%20%7B7,S%7D%20%7B8,S%7D%0A4%20O%20u0%20p2%20c0%20%7B2,S%7D%20%7B5,S%7D%0A5%20O%20u0%20p2%20c0%20%7B4,S%7D%20%7B9,S%7D%0A6%20H%20u0%20p0%20c0%20%7B3,S%7D%0A7%20H%20u0%20p0%20c0%20%7B3,S%7D%0A8%20H%20u0%20p0%20c0%20%7B3,S%7D%0A9%20H%20u0%20p0%20c0%20%7B5,S%7D%0A

both GA H298 estimates are about 20 kcal/mol lower than library H298 and the group values are:
O2s-O2s(Cds-O2d): -23.22 kcal/mol
O2s-OsH: -16.3 kcal/mol

Possible solution is to make new "zero" node to avoid adding O2s-OsH when we add O2s-O2s(Cds-O2d) group:

entry(
    index = 227800,
    label = "O2s-(Os-CdOd)H",
    group = 
"""
1 * O2s u0 {2,S} {3,S}
2   O2s u0 {1,S} {4,S}
3   H   u0 {1,S}
4   CO  u0 {2,S} {5,D}
5   O2d u0 {4,D}
""",
    thermo = ThermoData(
        Tdata = ([300,400,500,600,800,1000,1500],'K'),
        Cpdata = ([0,0,0,0,0,0,0],'cal/(mol*K)'),
        H298 = (0,'kcal/mol'),
        S298 = (0,'cal/(mol*K)'),
    ),
    shortDesc = """set to 0 to avoid double counting with O2s-O2s(Cds-O2d)""",
    longDesc = 
"""

""",
)

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the two linked molecule examples and compare their group-additivity H298 estimates with the library values, focusing on O2s-O2s(Cds-O2d) and O2s-OsH. Review the proposed zero node and confirm that the correction removes the double counting without changing unrelated estimates.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
databases
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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