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New PFAS thermal decomposition families #702

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75d8e79
Adding in folders for new PFAS families, copied from commit ce80adc3f…
Nora-Khalil Oct 20, 2025
3358540
retraining PFAS_Hydrolysis with newest data from Caroline, sent over …
Nora-Khalil Oct 20, 2025
1a724d9
PFAS dictionary added to recommended.py
Nora-Khalil Oct 21, 2025
e1e6761
Entry with index 19 (C2F5OCFHCF3 <=> C2F4O-2+C2HF5) was using species…
Nora-Khalil Oct 21, 2025
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232 changes: 232 additions & 0 deletions input/kinetics/families/CO2_Elimination_From_Carboxylic_Acid/groups.py
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Original file line number Diff line number Diff line change
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#!/usr/bin/env python
# encoding: utf-8

name = "CO2_Elimination_From_Carboxylic_Acid/groups"
shortDesc = ""
longDesc = """
*1R - F
\
*2C = *3O <=> *4O = *2C = *3O + F - *1R - *5H
/
*4O - *5H
"""

template(reactants=["Root"], products=["CO2", "R_H"], ownReverse=False)

reverse = "CO2_addition"
reversible = True

reactantNum = 1

productNum = 2

autoGenerated = True

recipe(actions=[
['BREAK_BOND', '*4', 1, '*5'],
['BREAK_BOND', '*2', 1, '*1'],
['CHANGE_BOND', '*4', 1, '*2'],
['FORM_BOND', '*5', 1, '*1'],
])

entry(
index = 0,
label = "Root",
group =
"""
1 *2 C u0 {2,S} {3,S} {4,D}
2 *1 R u[0,1,2] {1,S} {6,S}
3 *4 O u0 {1,S} {5,S}
4 *3 O u0 {1,D}
5 *5 H u0 {3,S}
6 [F1s,H] u0 {2,S}
""",
kinetics = None,
)

entry(
index = 1,
label = "Root_Ext-2R-R",
group =
"""
1 *2 C u0 {2,S} {3,S} {4,D}
2 *1 C u[0,1,2] {1,S} {6,S} {7,[S,B,D,T,Q]}
3 *4 O u0 {1,S} {5,S}
4 *3 O u0 {1,D}
5 *5 H u0 {3,S}
6 [F1s,H] u0 {2,S}
7 R!H ux {2,[S,B,D,T,Q]}
""",
kinetics = None,
)

entry(
index = 2,
label = "Root_Ext-2R-R_7R!H->F",
group =
"""
1 *2 C u0 {2,S} {3,S} {4,D}
2 *1 C u[0,1,2] {1,S} {6,S} {7,S}
3 *4 O u0 {1,S} {5,S}
4 *3 O u0 {1,D}
5 *5 H u0 {3,S}
6 [F1s,H] u0 {2,S}
7 F u0 r0 {2,S}
""",
kinetics = None,
)

entry(
index = 3,
label = "Root_Ext-2R-R_N-7R!H->F",
group =
"""
1 *2 C u0 {2,S} {3,S} {4,D}
2 *1 C u[0,1,2] {1,S} {6,S} {7,[S,B,D,T,Q]}
3 *4 O u0 {1,S} {5,S}
4 *3 O u0 {1,D}
5 *5 H u0 {3,S}
6 [F1s,H] u0 {2,S}
7 [Li,O,C,Si,Br,S,I,P,Cl,N] ux {2,[S,B,D,T,Q]}
""",
kinetics = None,
)

entry(
index = 4,
label = "Root_Ext-2R-R_N-7R!H->F_Ext-7BrCClILiNOPSSi-R_Ext-8R!H-R",
group =
"""
1 *2 C u0 {2,S} {3,S} {4,D}
2 *1 C u[0,1,2] {1,S} {6,S} {7,[S,B,D,T,Q]}
3 *4 O u0 {1,S} {5,S}
4 *3 O u0 {1,D}
5 *5 H u0 {3,S}
6 [F1s,H] u0 {2,S}
7 O ux {2,[S,B,D,T,Q]} {8,[S,B,D,T,Q]}
8 C ux {7,[S,B,D,T,Q]} {9,[S,B,D,T,Q]}
9 R!H ux {8,[S,B,D,T,Q]}
""",
kinetics = None,
)

entry(
index = 5,
label = "Root_Ext-2R-R_N-7R!H->F_Ext-7BrCClILiNOPSSi-R_Ext-8R!H-R_9R!H->C",
group =
"""
1 *2 C u0 {2,S} {3,S} {4,D}
2 *1 C u[0,1,2] {1,S} {6,S} {7,S}
3 *4 O u0 {1,S} {5,S}
4 *3 O u0 {1,D}
5 *5 H u0 {3,S}
6 [F1s,H] u0 {2,S}
7 O u0 {2,S} {8,S}
8 C u0 {7,S} {9,[S,B,D,T,Q]}
9 C ux {8,[S,B,D,T,Q]}
""",
kinetics = None,
)

entry(
index = 6,
label = "Root_Ext-2R-R_N-7R!H->F_Ext-7BrCClILiNOPSSi-R_Ext-8R!H-R_9R!H->C_6F1sH->H",
group =
"""
1 *2 C u0 {2,S} {3,S} {4,D}
2 *1 C u[0,1,2] {1,S} {6,S} {7,S}
3 *4 O u0 {1,S} {5,S}
4 *3 O u0 {1,D}
5 *5 H u0 {3,S}
6 H u0 {2,S}
7 O u0 r0 {2,S} {8,S}
8 C u0 r0 {7,S} {9,[S,B,D,T,Q]}
9 C ux {8,[S,B,D,T,Q]}
""",
kinetics = None,
)

entry(
index = 7,
label = "Root_Ext-2R-R_N-7R!H->F_Ext-7BrCClILiNOPSSi-R_Ext-8R!H-R_9R!H->C_N-6F1sH->H",
group =
"""
1 *2 C u0 {2,S} {3,S} {4,D}
2 *1 C u[0,1,2] {1,S} {6,S} {7,S}
3 *4 O u0 {1,S} {5,S}
4 *3 O u0 {1,D}
5 *5 H u0 {3,S}
6 F1s u0 {2,S}
7 O u0 r0 {2,S} {8,S}
8 C u0 r0 {7,S} {9,[S,B,D,T,Q]}
9 C ux {8,[S,B,D,T,Q]}
""",
kinetics = None,
)

entry(
index = 8,
label = "Root_Ext-2R-R_N-7R!H->F_Ext-7BrCClILiNOPSSi-R_Ext-8R!H-R_N-9R!H->C",
group =
"""
1 *2 C u0 r0 {2,S} {3,S} {4,D}
2 *1 C u1 r0 {1,S} {6,S} {7,[S,B,D,T,Q]}
3 *4 O u0 r0 {1,S} {5,S}
4 *3 O u0 r0 {1,D}
5 *5 H u0 r0 {3,S}
6 [F1s,H] u0 r0 {2,S}
7 O ux {2,[S,B,D,T,Q]} {8,[S,B,D,T,Q]}
8 C ux {7,[S,B,D,T,Q]} {9,S}
9 [F,Li,O,Si,Br,S,I,P,Cl,N] u0 r0 {8,S}
""",
kinetics = None,
)

entry(
index = 9,
label = "Root_Ext-2R-R_N-7R!H->F_6F1sH->H",
group =
"""
1 *2 C u0 {2,S} {3,S} {4,D}
2 *1 C u[0,1,2] {1,S} {6,S} {7,[S,B,D,T,Q]}
3 *4 O u0 {1,S} {5,S}
4 *3 O u0 {1,D}
5 *5 H u0 {3,S}
6 H u0 {2,S}
7 [Li,O,C,Si,Br,S,I,P,Cl,N] ux {2,[S,B,D,T,Q]}
""",
kinetics = None,
)

entry(
index = 10,
label = "Root_Ext-2R-R_N-7R!H->F_N-6F1sH->H",
group =
"""
1 *2 C u0 {2,S} {3,S} {4,D}
2 *1 C u[0,1,2] {1,S} {6,S} {7,[S,B,D,T,Q]}
3 *4 O u0 {1,S} {5,S}
4 *3 O u0 {1,D}
5 *5 H u0 {3,S}
6 F1s u0 {2,S}
7 [Li,O,C,Si,Br,S,I,P,Cl,N] ux {2,[S,B,D,T,Q]}
""",
kinetics = None,
)

tree(
"""
L1: Root
L2: Root_Ext-2R-R
L3: Root_Ext-2R-R_7R!H->F
L3: Root_Ext-2R-R_N-7R!H->F
L4: Root_Ext-2R-R_N-7R!H->F_Ext-7BrCClILiNOPSSi-R_Ext-8R!H-R
L5: Root_Ext-2R-R_N-7R!H->F_Ext-7BrCClILiNOPSSi-R_Ext-8R!H-R_9R!H->C
L6: Root_Ext-2R-R_N-7R!H->F_Ext-7BrCClILiNOPSSi-R_Ext-8R!H-R_9R!H->C_6F1sH->H
L6: Root_Ext-2R-R_N-7R!H->F_Ext-7BrCClILiNOPSSi-R_Ext-8R!H-R_9R!H->C_N-6F1sH->H
L5: Root_Ext-2R-R_N-7R!H->F_Ext-7BrCClILiNOPSSi-R_Ext-8R!H-R_N-9R!H->C
L4: Root_Ext-2R-R_N-7R!H->F_6F1sH->H
L4: Root_Ext-2R-R_N-7R!H->F_N-6F1sH->H
"""
)

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