Refit 1,3 sigmatropic rearrangement rate rules

ReactionMechanismGenerator · Mar 9, 2022 · e118363 · e118363
1 parent 1dff3d2
commit e118363
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diff --git a/input/kinetics/families/1,3_sigmatropic_rearrangement/groups.py b/input/kinetics/families/1,3_sigmatropic_rearrangement/groups.py
@@ -81,29 +81,29 @@
 
 entry(
     index = 3,
-    label = "Root_Ext-2R!H-R_5R!H->C_Ext-1R!H-R",
+    label = "Root_Ext-2R!H-R_5R!H->C_4R!H->C",
     group = 
 """
-1 *2 C   u0 {2,S} {3,D} {6,[S,D,T,B,Q]}
-2 *3 N   u0 r1 {1,S} {4,S} {5,[S,D,T,B,Q]}
+1 *2 C   u0 {2,S} {3,D}
+2 *3 N   u0 {1,S} {4,S} {5,[S,D,T,B,Q]}
 3 *1 R!H u0 {1,D}
-4 *4 R!H u0 r1 {2,S}
-5    C   ux r1 {2,[S,D,T,B,Q]}
-6    R!H ux {1,[S,D,T,B,Q]}
+4 *4 C   u0 {2,S}
+5    C   ux {2,[S,D,T,B,Q]}
 """,
     kinetics = None,
 )
 
 entry(
     index = 4,
-    label = "Root_Ext-2R!H-R_5R!H->C_4R!H->C",
+    label = "Root_Ext-2R!H-R_5R!H->C_4R!H->C_Ext-1R!H-R",
     group = 
 """
-1 *2 C   u0 {2,S} {3,D}
-2 *3 N   u0 {1,S} {4,S} {5,S}
-3 *1 R!H u0 {1,D}
-4 *4 C   u0 {2,S}
-5    C   u0 {2,S}
+1 *2 C   u0 r0 {2,S} {3,D} {6,[S,D,T,B,Q]}
+2 *3 N   u0 r1 {1,S} {4,S} {5,S}
+3 *1 R!H u0 r0 {1,D}
+4 *4 C   u0 r1 {2,S}
+5    C   u0 r1 {2,S}
+6    R!H ux {1,[S,D,T,B,Q]}
 """,
     kinetics = None,
 )
@@ -113,11 +113,11 @@
     label = "Root_Ext-2R!H-R_5R!H->C_4R!H->C_3R!H->N",
     group = 
 """
-1 *2 C u0 r0 {2,S} {3,D}
-2 *3 N u0 r1 {1,S} {4,S} {5,S}
-3 *1 N u0 r0 {1,D}
+1 *2 C u0 {2,S} {3,D}
+2 *3 N u0 r1 {1,S} {4,S} {5,[S,D,T,B,Q]}
+3 *1 N u0 {1,D}
 4 *4 C u0 r1 {2,S}
-5    C u0 r1 {2,S}
+5    C ux r1 {2,[S,D,T,B,Q]}
 """,
     kinetics = None,
 )
@@ -127,11 +127,11 @@
     label = "Root_Ext-2R!H-R_5R!H->C_4R!H->C_N-3R!H->N",
     group = 
 """
-1 *2 C u0 r0 {2,S} {3,D}
-2 *3 N u0 r1 {1,S} {4,S} {5,S}
-3 *1 O u0 r0 {1,D}
+1 *2 C u0 {2,S} {3,D}
+2 *3 N u0 r1 {1,S} {4,S} {5,[S,D,T,B,Q]}
+3 *1 O u0 {1,D}
 4 *4 C u0 r1 {2,S}
-5    C u0 r1 {2,S}
+5    C ux r1 {2,[S,D,T,B,Q]}
 """,
     kinetics = None,
 )
@@ -269,7 +269,7 @@
 2 *3 N                      u0 r1 {1,S} {4,S}
 3 *1 N                      u0 r1 {1,D}
 4 *4 C                      u0 r1 {2,S} {5,D}
-5    [F,I,N,Br,Cl,O,P,S,Si] u0 r1 {4,D}
+5    [I,P,Br,Cl,O,F,N,S,Si] u0 r1 {4,D}
 """,
     kinetics = None,
 )
@@ -350,7 +350,7 @@
 2 *3 O                      u0 r1 {1,S} {4,S}
 3 *1 N                      u0 r1 {1,D}
 4 *4 C                      u0 r1 {2,S} {5,D}
-5    [F,I,N,Br,Cl,O,P,S,Si] u0 r1 {4,D}
+5    [I,P,Br,Cl,O,F,N,S,Si] u0 r1 {4,D}
 """,
     kinetics = None,
 )
@@ -390,7 +390,7 @@
 2 *3 R!H u0 {1,S} {4,S}
 3 *1 R!H u0 {1,D}
 4 *4 C   u0 {2,S} {5,[S,D,T,B,Q]}
-5    R!H ux {4,[S,D,T,B,Q]}
+5    O   ux {4,[S,D,T,B,Q]}
 """,
     kinetics = None,
 )
@@ -400,20 +400,6 @@
     label = "Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N",
     group = 
 """
-1 *2 C   u0 r0 {2,S} {3,D}
-2 *3 N   u0 {1,S} {4,S}
-3 *1 O   u0 {1,D}
-4 *4 C   u0 {2,S} {5,[S,D,T,B,Q]}
-5    R!H ux {4,[S,D,T,B,Q]}
-""",
-    kinetics = None,
-)
-
-entry(
-    index = 27,
-    label = "Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_5R!H->O",
-    group = 
-"""
 1 *2 C u0 r0 {2,S} {3,D}
 2 *3 N u0 {1,S} {4,S}
 3 *1 O u0 {1,D}
@@ -424,123 +410,51 @@
 )
 
 entry(
-    index = 28,
-    label = "Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_5R!H->O_Ext-4R!H-R",
-    group = 
-"""
-1 *2 C   u0 r0 {2,S} {3,D}
-2 *3 N   u0 {1,S} {4,S}
-3 *1 O   u0 {1,D}
-4 *4 C   u0 {2,S} {5,D} {6,[S,D,T,B,Q]}
-5    O   u0 r0 {4,D}
-6    R!H ux {4,[S,D,T,B,Q]}
-""",
-    kinetics = None,
-)
-
-entry(
-    index = 29,
-    label = "Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_5R!H->O_Ext-1R!H-R",
+    index = 27,
+    label = "Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_Ext-1R!H-R",
     group = 
 """
 1 *2 C   u0 r0 {2,S} {3,D} {6,[S,D,T,B,Q]}
-2 *3 N   u0 {1,S} {4,S}
-3 *1 O   u0 {1,D}
-4 *4 C   u0 {2,S} {5,[S,D,T,B,Q]}
+2 *3 N   u0 r0 {1,S} {4,S}
+3 *1 O   u0 r0 {1,D}
+4 *4 C   u0 r0 {2,S} {5,[S,D,T,B,Q]}
 5    O   ux {4,[S,D,T,B,Q]}
 6    R!H ux {1,[S,D,T,B,Q]}
 """,
     kinetics = None,
 )
 
 entry(
-    index = 30,
-    label = "Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_N-5R!H->O",
-    group = 
-"""
-1 *2 C u0 r0 {2,S} {3,D}
-2 *3 N u0 r0 {1,S} {4,S}
-3 *1 O u0 r0 {1,D}
-4 *4 C u0 r0 {2,S} {5,D}
-5    N ux {4,D}
-""",
-    kinetics = None,
-)
-
-entry(
-    index = 31,
+    index = 28,
     label = "Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N",
     group = 
 """
-1 *2 C   u0 r0 {2,S} {3,D}
-2 *3 O   u0 {1,S} {4,S}
-3 *1 N   u0 {1,D}
-4 *4 C   u0 {2,S} {5,[S,D,T,B,Q]}
-5    R!H u0 {4,[S,D,T,B,Q]}
-""",
-    kinetics = None,
-)
-
-entry(
-    index = 32,
-    label = "Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_5R!H->N",
-    group = 
-"""
 1 *2 C u0 r0 {2,S} {3,D}
 2 *3 O u0 {1,S} {4,S}
 3 *1 N u0 {1,D}
 4 *4 C u0 {2,S} {5,[S,D,T,B,Q]}
-5    N u0 {4,[S,D,T,B,Q]}
-""",
-    kinetics = None,
-)
-
-entry(
-    index = 33,
-    label = "Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_5R!H->N_Ext-4R!H-R",
-    group = 
-"""
-1 *2 C   u0 r0 {2,S} {3,D}
-2 *3 O   u0 {1,S} {4,S}
-3 *1 N   u0 {1,D}
-4 *4 C   u0 {2,S} {5,[S,D,T,B,Q]} {6,[S,D,T,B,Q]}
-5    N   u0 r0 {4,[S,D,T,B,Q]}
-6    R!H ux {4,[S,D,T,B,Q]}
-""",
-    kinetics = None,
-)
-
-entry(
-    index = 34,
-    label = "Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_N-5R!H->N",
-    group = 
-"""
-1 *2 C u0 r0 {2,S} {3,D}
-2 *3 O u0 {1,S} {4,S}
-3 *1 N u0 {1,D}
-4 *4 C u0 {2,S} {5,D}
-5    O u0 {4,D}
+5    O ux {4,[S,D,T,B,Q]}
 """,
     kinetics = None,
 )
 
 entry(
-    index = 35,
-    label = "Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_N-5R!H->N_Ext-1R!H-R",
+    index = 29,
+    label = "Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_Ext-1R!H-R",
     group = 
 """
 1 *2 C   u0 r0 {2,S} {3,D} {6,[S,D,T,B,Q]}
-2 *3 O   u0 {1,S} {4,S}
-3 *1 N   u0 {1,D}
-4 *4 C   u0 {2,S} {5,D}
-5    O   u0 r0 {4,D}
+2 *3 O   u0 r0 {1,S} {4,S}
+3 *1 N   u0 r0 {1,D}
+4 *4 C   u0 r0 {2,S} {5,[S,D,T,B,Q]}
+5    O   ux {4,[S,D,T,B,Q]}
 6    R!H ux {1,[S,D,T,B,Q]}
 """,
     kinetics = None,
 )
 
 entry(
-    index = 36,
+    index = 30,
     label = "Root_N-1R!H-inRing_2R!H->C",
     group = 
 """
@@ -553,7 +467,7 @@
 )
 
 entry(
-    index = 37,
+    index = 31,
     label = "Root_N-1R!H-inRing_N-2R!H->C",
     group = 
 """
@@ -570,8 +484,8 @@
 L1: Root
     L2: Root_Ext-2R!H-R
         L3: Root_Ext-2R!H-R_5R!H->C
-            L4: Root_Ext-2R!H-R_5R!H->C_Ext-1R!H-R
             L4: Root_Ext-2R!H-R_5R!H->C_4R!H->C
+                L5: Root_Ext-2R!H-R_5R!H->C_4R!H->C_Ext-1R!H-R
                 L5: Root_Ext-2R!H-R_5R!H->C_4R!H->C_3R!H->N
                 L5: Root_Ext-2R!H-R_5R!H->C_4R!H->C_N-3R!H->N
             L4: Root_Ext-2R!H-R_5R!H->C_N-4R!H->C
@@ -594,15 +508,9 @@
     L2: Root_N-1R!H-inRing
         L3: Root_N-1R!H-inRing_Ext-4R!H-R
             L4: Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N
-                L5: Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_5R!H->O
-                    L6: Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_5R!H->O_Ext-4R!H-R
-                    L6: Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_5R!H->O_Ext-1R!H-R
-                L5: Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_N-5R!H->O
+                L5: Root_N-1R!H-inRing_Ext-4R!H-R_2R!H->N_Ext-1R!H-R
             L4: Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N
-                L5: Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_5R!H->N
-                    L6: Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_5R!H->N_Ext-4R!H-R
-                L5: Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_N-5R!H->N
-                    L6: Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_N-5R!H->N_Ext-1R!H-R
+                L5: Root_N-1R!H-inRing_Ext-4R!H-R_N-2R!H->N_Ext-1R!H-R
         L3: Root_N-1R!H-inRing_2R!H->C
         L3: Root_N-1R!H-inRing_N-2R!H->C
 """