Merge pull request #205 from ReactionMechanismGenerator/Aromatics_upd…

…ates_1

Aromatics updates 1 (out of 4): Propargyl radical recombination to benzene

input/kinetics/families/6_membered_central_C-C_shift/groups.py

@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "6_membered_central_C-C_shift/groups"
+shortDesc = u"Concerted shift of the central C-C bond in an 1,5-unsaturated hexane to between the end atoms"
+longDesc = u"""
+Taken from:
+
+Miller, J. A.; Klippenstein, S. J., The Recombination of Propargyl Radicals and Other Reactions on a C6H6 Potential.
+J. Phys. Chem. A 2003, 107, 7783-7799.
+"""
+
+template(reactants=["1_5_unsaturated_hexane"], products=["1_5_unsaturated_hexane"], ownReverse=True)
+
+recipe(actions=[
+    ['BREAK_BOND', '*3', 1, '*4'],
+    ['CHANGE_BOND', '*1', -1, '*2'],
+    ['CHANGE_BOND', '*5', -1, '*6'],
+    ['CHANGE_BOND', '*2', 1, '*3'],
+    ['CHANGE_BOND', '*4', 1, '*5'],
+    ['FORM_BOND', '*1', 1, '*6'],
+])
+
+boundaryAtoms = ["*1", "*6"]
+
+entry(
+    index = 1,
+    label = "1_5_unsaturated_hexane",
+    group=
+    """
+    1 *3 C u0 {2,S} {3,[S,D]}
+    2 *4 C u0 {1,S} {4,[S,D]}
+    3 *2 C u0 {1,[S,D]} {5,[D,T]}
+    4 *5 C u0 {2,[S,D]} {6,[D,T]}
+    5 *1 C u0 {3,[D,T]}
+    6 *6 C u0 {4,[D,T]}
+    """,
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label = "1_5_hexadiyne",
+    group=
+"""
+1 *3 C u0 {2,S} {3,S}
+2 *4 C u0 {1,S} {4,S}
+3 *2 Ct u0 {1,S} {5,T}
+4 *5 Ct u0 {2,S} {6,T}
+5 *1 Ct u0 {3,T}
+6 *6 Ct u0 {4,T}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label = "1_2_4_5_hexatetraene",
+    group=
+"""
+1 *3 Cd u0 {2,S} {3,D}
+2 *4 Cd u0 {1,S} {4,D}
+3 *2 Cdd u0 {1,D} {5,D}
+4 *5 Cdd u0 {2,D} {6,D}
+5 *1 C u0 {3,D}
+6 *6 C u0 {4,D}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label = "1_5_hexadiene",
+    group=
+"""
+1 *3 C u0 {2,S} {3,S}
+2 *4 C u0 {1,S} {4,S}
+3 *2 Cd u0 {1,S} {5,D}
+4 *5 Cd u0 {2,S} {6,D}
+5 *1 C u0 {3,D}
+6 *6 C u0 {4,D}
+""",
+    kinetics = None,
+)
+
+tree(
+"""
+L1: 1_5_unsaturated_hexane
+    L2: 1_5_hexadiyne
+    L2: 1_2_4_5_hexatetraene
+    L2: 1_5_hexadiene
+"""
+)
+

input/kinetics/families/6_membered_central_C-C_shift/rules.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "6_membered_central_C-C_shift/rules"
+shortDesc = u"Concerted shift of the central C-C bond in an 1,5-unsaturated hexane to between the end atoms"
+longDesc = u"""
+Taken from:
+
+Miller, J. A.; Klippenstein, S. J., The Recombination of Propargyl Radicals and Other Reactions on a C6H6 Potential.
+J. Phys. Chem. A 2003, 107, 7783-7799.
+"""
+

input/kinetics/families/6_membered_central_C-C_shift/training/dictionary.txt

@@ -0,0 +1,56 @@
+C6H6-4
+1  *1 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
+2  *6 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
+3  *2 C u0 p0 c0 {1,S} {5,T}
+4  *5 C u0 p0 c0 {2,S} {6,T}
+5  *3 C u0 p0 c0 {3,T} {11,S}
+6  *4 C u0 p0 c0 {4,T} {12,S}
+7     H u0 p0 c0 {1,S}
+8     H u0 p0 c0 {1,S}
+9     H u0 p0 c0 {2,S}
+10    H u0 p0 c0 {2,S}
+11    H u0 p0 c0 {5,S}
+12    H u0 p0 c0 {6,S}
+
+C6H6
+1  *3 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
+2  *4 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
+3  *2 C u0 p0 c0 {1,S} {5,T}
+4  *5 C u0 p0 c0 {2,S} {6,T}
+5  *1 C u0 p0 c0 {3,T} {11,S}
+6  *6 C u0 p0 c0 {4,T} {12,S}
+7     H u0 p0 c0 {1,S}
+8     H u0 p0 c0 {1,S}
+9     H u0 p0 c0 {2,S}
+10    H u0 p0 c0 {2,S}
+11    H u0 p0 c0 {5,S}
+12    H u0 p0 c0 {6,S}
+
+C6H6-2
+1  *1 C u0 p0 c0 {2,S} {5,D} {7,S}
+2  *6 C u0 p0 c0 {1,S} {6,D} {8,S}
+3  *3 C u0 p0 c0 {5,D} {9,S} {10,S}
+4  *4 C u0 p0 c0 {6,D} {11,S} {12,S}
+5  *2 C u0 p0 c0 {1,D} {3,D}
+6  *5 C u0 p0 c0 {2,D} {4,D}
+7     H u0 p0 c0 {1,S}
+8     H u0 p0 c0 {2,S}
+9     H u0 p0 c0 {3,S}
+10    H u0 p0 c0 {3,S}
+11    H u0 p0 c0 {4,S}
+12    H u0 p0 c0 {4,S}
+
+C6H6-3
+1  *3 C u0 p0 c0 {2,S} {5,D} {7,S}
+2  *4 C u0 p0 c0 {1,S} {6,D} {8,S}
+3  *1 C u0 p0 c0 {5,D} {9,S} {10,S}
+4  *6 C u0 p0 c0 {6,D} {11,S} {12,S}
+5  *2 C u0 p0 c0 {1,D} {3,D}
+6  *5 C u0 p0 c0 {2,D} {4,D}
+7     H u0 p0 c0 {1,S}
+8     H u0 p0 c0 {2,S}
+9     H u0 p0 c0 {3,S}
+10    H u0 p0 c0 {3,S}
+11    H u0 p0 c0 {4,S}
+12    H u0 p0 c0 {4,S}
+

input/kinetics/families/6_membered_central_C-C_shift/training/reactions.py

@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "6_membered_central_C-C_shift/training"
+shortDesc = u"Kinetics used to train group additivity values"
+longDesc = u"""
+Put kinetic parameters for reactions to use as a training set for fitting
+group additivity values in this file.
+"""
+
+entry(
+    index = 1,
+    label = "C6H6 <=> C6H6-2",
+    degeneracy = 1,
+    kinetics = Arrhenius(A=(2.30946e+10, 's^-1'), n=0.360276, Ea=(144.706, 'kJ/mol'), T0=(1, 'K')),
+    rank = 3,
+    shortDesc = u"""Training reaction from kinetics library: 2003_Miller_Propargyl_Recomb_High_P""",
+    longDesc = 
+u"""
+Taken from entry: I <=> II
+""",
+)
+
+
+
+entry(
+    index = 2,
+    label = "C6H6-3 <=> C6H6-4",
+    degeneracy = 1,
+    kinetics = Arrhenius(A=(9.06322e+11, 's^-1'), n=-0.0265989, Ea=(166.561, 'kJ/mol'), T0=(1, 'K')),
+    rank = 3,
+    shortDesc = u"""Training reaction from kinetics library: 2003_Miller_Propargyl_Recomb_High_P_reverse""",
+    longDesc = 
+u"""
+Taken from entry: II <=> I
+""",
+)
+

input/kinetics/families/Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH/groups.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH/groups"
+shortDesc = u"Intramolecular ring-closure by concerted addition of two alkene end groups in  a 1_3_hexadien_5_yne backbone " \
+            u"(C=C-C=C-C#C) with simultaneous 1,2-H shift over an unsaturated bond to form an unsaturated singlet carbene " \
+            u"cyclohexane product"
+longDesc = u"""
+From 2003 Miller and Klippenstein Propargyl recombination PES:
+
+Miller, J. A.; Klippenstein, S. J., The Recombination of Propargyl Radicals and Other Reactions on a C6H6 Potential.
+J. Phys. Chem. A 2003, 107, 7783-7799.
+"""
+
+template(reactants=["1_3_hexadien_5_yne"], products=["unsaturated_singlet_carbene_cyclohexane"], ownReverse=False)
+
+reverse = "Concerted_Retro_Intra_Diels_alder_monocyclic_singlet_carbene_disproportionation"
+
+recipe(actions=[
+    ['CHANGE_BOND', '*1', -1, '*2'],
+    ['CHANGE_BOND', '*3', -1, '*4'],
+    ['CHANGE_BOND', '*2', 1, '*3'],
+    ['CHANGE_BOND', '*5', -1, '*6'],
+    ['CHANGE_BOND', '*4', 1, '*5'],
+    ['FORM_BOND', '*1', 1, '*6'],
+    ['CHANGE_BOND', '*5', -1, '*6'],
+    ['BREAK_BOND', '*6', 1, '*7'],
+    ['FORM_BOND', '*5', 1, '*7'],
+    ['GAIN_PAIR', '*6', '1'],
+])
+
+boundaryAtoms = ["*1", "*7"]
+
+entry(
+    index = 1,
+    label = "1_3_hexadien_5_yne",
+    group = 'OR{linear_1_3_hexadien_5_yne}',
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label = "linear_1_3_hexadien_5_yne",
+    group =
+"""
+1  *3 Cd u0 {2,S} {3,D} {8,S}
+2  *2 Cd u0 {1,S} {4,D} {7,S}
+3  *4 Cd u0 {1,D} {5,S} {9,S}
+4  *1 Cd u0 {2,D} {11,S} {12,S}
+5  *5 Ct u0 {3,S} {6,T}
+6  *6 Ct u0 p0 {5,T} {10,S}
+7 R u0 {2,S}
+8 R u0 {1,S}
+9 R u0 {3,S}
+10  *7 H u0 {6,S}
+11 R u0 {4,S}
+12 R u0 {4,S}
+""",
+    kinetics = None,
+)
+
+tree(
+"""
+L1: 1_3_hexadien_5_yne
+    L2: linear_1_3_hexadien_5_yne
+"""
+)
+

input/kinetics/families/Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH/rules.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH/groups"
+shortDesc = u"Intramolecular ring-closure by concerted addition of two alkene end groups in  a 1_3_hexadien_5_yne backbone " \
+            u"(C=C-C=C-C#C) with simultaneous 1,2-H shift over an unsaturated bond to form an unsaturated singlet carbene " \
+            u"cyclohexane product"
+longDesc = u"""
+From 2003 Miller and Klippenstein Propargyl recombination PES:
+
+Miller, J. A.; Klippenstein, S. J., The Recombination of Propargyl Radicals and Other Reactions on a C6H6 Potential.
+J. Phys. Chem. A 2003, 107, 7783-7799.
+"""
+

input/kinetics/families/Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH/training/dictionary.txt

@@ -0,0 +1,28 @@
+C6H6
+1  *3 C u0 p0 c0 {2,S} {3,D} {7,S}
+2  *2 C u0 p0 c0 {1,S} {4,D} {8,S}
+3  *4 C u0 p0 c0 {1,D} {5,S} {9,S}
+4  *1 C u0 p0 c0 {2,D} {10,S} {11,S}
+5  *5 C u0 p0 c0 {3,S} {6,T}
+6  *6 C u0 p0 c0 {5,T} {12,S}
+7     H u0 p0 c0 {1,S}
+8     H u0 p0 c0 {2,S}
+9     H u0 p0 c0 {3,S}
+10    H u0 p0 c0 {4,S}
+11    H u0 p0 c0 {4,S}
+12 *7 H u0 p0 c0 {6,S}
+
+C6H6-2
+1  *1 C u0 p0 c0 {2,S} {6,S} {7,S} {8,S}
+2  *2 C u0 p0 c0 {1,S} {3,D} {9,S}
+3  *3 C u0 p0 c0 {2,D} {4,S} {10,S}
+4  *4 C u0 p0 c0 {3,S} {5,D} {11,S}
+5  *5 C u0 p0 c0 {4,D} {6,S} {12,S}
+6  *6 C u0 p1 c0 {1,S} {5,S}
+7     H u0 p0 c0 {1,S}
+8     H u0 p0 c0 {1,S}
+9     H u0 p0 c0 {2,S}
+10    H u0 p0 c0 {3,S}
+11    H u0 p0 c0 {4,S}
+12 *7 H u0 p0 c0 {5,S}
+

input/kinetics/families/Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH/training/reactions.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH/training"
+shortDesc = u"Kinetics used to train group additivity values"
+longDesc = u"""
+Put kinetic parameters for reactions to use as a training set for fitting
+group additivity values in this file.
+"""
+
+entry(
+    index = 1,
+    label = "C6H6 <=> C6H6-2",
+    degeneracy = 1,
+    kinetics = Arrhenius(A=(2.65505e+13, 's^-1'), n=-0.215087, Ea=(217.397, 'kJ/mol'), T0=(1, 'K')),
+    rank = 3,
+    shortDesc = u"""Training reaction from kinetics library: 2003_Miller_Propargyl_Recomb_High_P""",
+    longDesc = 
+u"""
+Taken from entry: VIII <=> IX
+""",
+)
+

input/kinetics/families/Cyclopentadiene_scission/groups.py

@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Cyclopentadiene_scission/groups"
+shortDesc = u"Scission of one of the adjacent single bonds in a CPD subunit to form a conjugated singlet carbene"
+longDesc = u"""
+Currently, family will only scission a fused CPD + cyclopropane bicyclic subunit using calculated kinetics from 2003
+Miller and Klippenstein Propargyl recombination PES. Data needed before other entries can be added (e.g., simple CPD
+scission)
+"""
+
+template(reactants=["CPD_backbone"], products=["conjugated_singlet_carbene"], ownReverse=False)
+
+reverse = "Intra_singlet_carbene_addition"
+
+recipe(actions=[
+    ['BREAK_BOND', '*1', 1, '*2'],
+    ['CHANGE_BOND', '*2', -1, '*3'],
+    ['CHANGE_BOND', '*4', -1, '*5'],
+    ['CHANGE_BOND', '*1', 1, '*5'],
+    ['CHANGE_BOND', '*4', 1, '*3'],
+    ['GAIN_PAIR', '*2', '1']
+])
+
+boundaryAtoms = ["*1", "*2"]
+
+entry(
+    index = 1,
+    label = "CPD_backbone",
+    group ='OR{fused_CPD_cyclopropane_bicyclic}',
+    kinetics = None,
+)
+
+entry(
+    index = 2,
+    label = "fused_CPD_cyclopropane_bicyclic",
+    group =
+"""
+1 *1 C u0 {2,S} {5,S} {6,S}
+2 *2 Cd u0 {1,S} {3,D} {6,S}
+3 *3 Cd u0 {2,D} {4,S}
+4 *4 Cd u0 {3,S} {5,D}
+5 *5 Cd u0 {1,S} {4,D}
+6 C u0 {1,S} {2,S}
+""",
+    kinetics = None,
+)
+
+tree(
+"""
+L1: CPD_backbone
+    L2: fused_CPD_cyclopropane_bicyclic
+"""
+)
+