diff --git a/input/forbiddenStructures.py b/input/forbiddenStructures.py index f0e3484e71..e2ae305493 100644 --- a/input/forbiddenStructures.py +++ b/input/forbiddenStructures.py @@ -1,6 +1,8 @@ #!/usr/bin/env python # encoding: utf-8 +# IMPORTANT REQUEST: If you add a globally forbidden group, please comment why it is forbidden and give example\s. + name = "" shortDesc = u"" longDesc = u""" @@ -35,37 +37,6 @@ """, ) -entry( - label = "N_monorad_3singleBonds", - group = -""" -1 N u1 p0 {2,S} {3,S} {4,S} -2 R ux {1,S} -3 R ux {1,S} -4 R ux {1,S} -""", - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - label = "N_birad_singlet_2singleBonds", - group = -""" -1 N u0 p1 {2,S} {3,S} -2 R ux {1,S} -3 R ux {1,S} -""", - shortDesc = u"""""", - longDesc = -u""" - -""", -) - entry( label = "N_birad_triplet_2singleBonds", group = @@ -168,34 +139,6 @@ """, ) -entry( - label = "Carbene_D_triplet", - group = -""" -1 C u2 p0 {2,D} -2 C u0 {1,D} -""", - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - label = "Carbene_D_singlet", - group = -""" -1 C u0 p1 {2,D} -2 C u0 {1,D} -""", - shortDesc = u"""""", - longDesc = -u""" - -""", -) - entry( label = "Carbene_S_triplet", group = @@ -210,20 +153,6 @@ """, ) -entry( - label = "Carbene_S_singlet", - group = -""" -1 C u0 p1 {2,S} -2 R!H u0 {1,S} -""", - shortDesc = u"""""", - longDesc = -u""" - -""", -) - entry( label = "O3", group = diff --git a/input/kinetics/libraries/Ethylamine/dictionary.txt b/input/kinetics/libraries/Ethylamine/dictionary.txt new file mode 100644 index 0000000000..2d7e7f4997 --- /dev/null +++ b/input/kinetics/libraries/Ethylamine/dictionary.txt @@ -0,0 +1,193 @@ +NCC +1 N u0 p1 c0 {2,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {3,S} {6,S} {7,S} +3 C u0 p0 c0 {2,S} {8,S} {9,S} {10,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {3,S} +9 H u0 p0 c0 {3,S} +10 H u0 p0 c0 {3,S} + +CH2CH2NH2 +multiplicity 2 +1 C u1 p0 c0 {2,S} {3,S} {4,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 C u0 p0 c0 {1,S} {5,S} {6,S} {7,S} +5 N u0 p1 c0 {4,S} {8,S} {9,S} +6 H u0 p0 c0 {4,S} +7 H u0 p0 c0 {4,S} +8 H u0 p0 c0 {5,S} +9 H u0 p0 c0 {5,S} + +CH3CHNH2 +multiplicity 2 +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u1 p0 c0 {1,S} {3,S} {4,S} +3 H u0 p0 c0 {2,S} +4 N u0 p1 c0 {2,S} {8,S} {9,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {4,S} +9 H u0 p0 c0 {4,S} + +CH3CH2NH +multiplicity 2 +1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S} +2 C u0 p0 c0 {1,S} {3,S} {8,S} {9,S} +3 N u1 p1 c0 {2,S} {4,S} +4 H u0 p0 c0 {3,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {1,S} +8 H u0 p0 c0 {2,S} +9 H u0 p0 c0 {2,S} + +H +multiplicity 2 +1 H u1 p0 c0 + +H2 +1 H u0 p0 c0 {2,S} +2 H u0 p0 c0 {1,S} + +CH3 +multiplicity 2 +1 C u1 p0 c0 {2,S} {3,S} {4,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} + +CH4 +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} + +NH2 +multiplicity 2 +1 N u1 p1 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} + +NH3 +1 N u0 p1 c0 {2,S} {3,S} {4,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} + +C2H4 +1 C u0 p0 c0 {2,D} {3,S} {4,S} +2 C u0 p0 c0 {1,D} {5,S} {6,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {2,S} + +CH2CHNH2 +1 C u0 p0 c0 {2,S} {3,S} {4,D} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 C u0 p0 c0 {1,D} {5,S} {6,S} +5 N u0 p1 c0 {4,S} {7,S} {8,S} +6 H u0 p0 c0 {4,S} +7 H u0 p0 c0 {5,S} +8 H u0 p0 c0 {5,S} + +CH2NH +1 C u0 p0 c0 {2,S} {3,S} {4,D} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 N u0 p1 c0 {1,D} {5,S} +5 H u0 p0 c0 {4,S} + +CH2NH2 +multiplicity 2 +1 C u1 p0 c0 {2,S} {3,S} {4,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 N u0 p1 c0 {1,S} {5,S} {6,S} +5 H u0 p0 c0 {4,S} +6 H u0 p0 c0 {4,S} + +N2H4 +1 N u0 p1 c0 {2,S} {3,S} {4,S} +2 N u0 p1 c0 {1,S} {5,S} {6,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {2,S} + +N2H3 +multiplicity 2 +1 N u0 p1 c0 {2,S} {4,S} {5,S} +2 N u1 p1 c0 {1,S} {3,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} + +CH2CHNH +multiplicity 2 +1 C u1 p0 c0 {2,S} {3,S} {4,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 C u0 p0 c0 {1,S} {5,D} {6,S} +5 N u0 p1 c0 {4,D} {7,S} +6 H u0 p0 c0 {4,S} +7 H u0 p0 c0 {5,S} + +CH3CHN +multiplicity 2 +1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {3,D} {7,S} +3 N u1 p1 c0 {2,D} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} + +CH2CNH +1 C u0 p0 c0 {2,D} {4,S} {5,S} +2 C u0 p0 c0 {1,D} {3,D} +3 N u0 p1 c0 {2,D} {6,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {3,S} + +CH3CHNH +1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {3,D} {7,S} +3 N u0 p1 c0 {2,D} {8,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} +7 H u0 p0 c0 {2,S} +8 H u0 p0 c0 {3,S} + +HCN +1 C u0 p0 c0 {2,S} {3,T} +2 H u0 p0 c0 {1,S} +3 N u0 p1 c0 {1,T} + +CH3CN +1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S} +2 C u0 p0 c0 {1,S} {3,T} +3 N u0 p1 c0 {2,T} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +6 H u0 p0 c0 {1,S} + +OH +multiplicity 2 +1 O u1 p2 c0 {2,S} +2 H u0 p0 c0 {1,S} + +H2O +1 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} + diff --git a/input/kinetics/libraries/Ethylamine/reactions.py b/input/kinetics/libraries/Ethylamine/reactions.py new file mode 100644 index 0000000000..dee7248f60 --- /dev/null +++ b/input/kinetics/libraries/Ethylamine/reactions.py @@ -0,0 +1,229 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "Ethylamine" +shortDesc = u"" +longDesc = u""" +Automated Reaction Mechanism Generation Including Heteroatoms: Nitrogen +Alon Grinberg Dana, Beat Buesser, Shamel S. Merchant, William H. Green +Table 2 +Kinetic data for reactions 1–3, 7–24 were calculated at the CBS-QB3 level of theory with a 1d-HR correction. +Kinetic data for reactions 4–6 were adopted from the literature [http://dx.doi.org/10.1021/jp411141ws43, http://dx.doi.org/10.1021/ct7002786]. +""" + +entry( + index = 1, + label = "NCC + H <=> CH2CH2NH2 + H2", + degeneracy = 1, + kinetics = Arrhenius(A=(9.07e+04, 'cm^3/(mol*s)'), n=2.75, Ea=(6800, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R1: EA H abstraction""", +) + +entry( + index = 2, + label = "NCC + H <=> CH3CHNH2 + H2", + degeneracy = 1, + kinetics = Arrhenius(A=(9.54e+03, 'cm^3/(mol*s)'), n=2.94, Ea=(500, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R2: EA H abstraction""", +) + +entry( + index = 3, + label = "NCC + H <=> CH3CH2NH + H2", + degeneracy = 1, + kinetics = Arrhenius(A=(8.04e+04, 'cm^3/(mol*s)'), n=2.64, Ea=(5500, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R3: EA H abstraction""", +) + +entry( + index = 4, + label = "NCC + CH3 <=> CH2CH2NH2 + CH4", + degeneracy = 1, + kinetics = Arrhenius(A=(3.28e-04, 'cm^3/(mol*s)'), n=4.85, Ea=(7000, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R4: EA H abstraction""", +) + +entry( + index = 5, + label = "NCC + CH3 <=> CH3CHNH2 + CH4", + degeneracy = 1, + kinetics = Arrhenius(A=(2.76e-02, 'cm^3/(mol*s)'), n=4.23, Ea=(4200, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R5: EA H abstraction""", +) + +entry( + index = 6, + label = "NCC + CH3 <=> CH3CH2NH + CH4", + degeneracy = 1, + kinetics = Arrhenius(A=(1.27e-02, 'cm^3/(mol*s)'), n=4.41, Ea=(4800, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R6: EA H abstraction""", +) + +entry( + index = 7, + label = "NCC + NH2 <=> CH2CH2NH2 + NH3", + degeneracy = 1, + kinetics = Arrhenius(A=(1.44e-02, 'cm^3/(mol*s)'), n=4.43, Ea=(3600, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R7: EA H abstraction""", +) + +entry( + index = 8, + label = "NCC + NH2 <=> CH3CHNH2 + NH3", + degeneracy = 1, + kinetics = Arrhenius(A=(1.28e+00, 'cm^3/(mol*s)'), n=3.75, Ea=(1000, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R8: EA H abstraction""", +) + +entry( + index = 9, + label = "NCC + NH2 <=> CH3CH2NH + NH3", + degeneracy = 1, + kinetics = Arrhenius(A=(9.73e-02, 'cm^3/(mol*s)'), n=4.03, Ea=(1900, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R9: EA H abstraction""", +) + +entry( + index = 10, + label = "NCC + OH <=> CH2CH2NH2 + H2O", + degeneracy = 1, + kinetics = Arrhenius(A=(7.94e+02, 'cm^3/(mol*s)'), n=2.97, Ea=(-1040, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R10: EA H abstraction""", +) + +entry( + index = 11, + label = "NCC + OH <=> CH3CHNH2 + H2O", + degeneracy = 1, + kinetics = Arrhenius(A=(3.28e+05, 'cm^3/(mol*s)'), n=2.24, Ea=(-3040, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R11: EA H abstraction""", +) + +entry( + index = 12, + label = "NCC + OH <=> CH3CH2NH + H2O", + degeneracy = 1, + kinetics = Arrhenius(A=(1.12e+05, 'cm^3/(mol*s)'), n=2.36, Ea=(-2860, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R12: EA H abstraction""", +) + +entry( + index = 13, + label = "N2H4 + H <=> N2H3 + H2", + degeneracy = 1, + kinetics = Arrhenius(A=(1.48e+08, 'cm^3/(mol*s)'), n=1.69, Ea=(4000, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R13: H abstraction""", +) + +entry( + index = 14, + label = "N2H4 + CH3 <=> N2H3 + CH4", + degeneracy = 1, + kinetics = Arrhenius(A=(1.77e+01, 'cm^3/(mol*s)'), n=3.60, Ea=(3500, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R14: H abstraction""", +) + +entry( + index = 15, + label = "N2H4 + NH2 <=> N2H3 + NH3", + degeneracy = 1, + kinetics = Arrhenius(A=(2.59e+03, 'cm^3/(mol*s)'), n=2.83, Ea=(700, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R15: H abstraction""", +) + +entry( + index = 16, + label = "CH3CHNH + H <=> CH2CHNH + H2", + degeneracy = 1, + kinetics = Arrhenius(A=(3.98e+04, 'cm^3/(mol*s)'), n=2.76, Ea=(4400, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R16: H abstraction""", +) + +entry( + index = 17, + label = "CH3CHNH + H <=> CH3CHN + H2", + degeneracy = 1, + kinetics = Arrhenius(A=(1.19e+07, 'cm^3/(mol*s)'), n=1.96, Ea=(2400, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R17: H abstraction""", +) + +entry( + index = 18, + label = "CH2CHNH2 + H <=> CH2CH2NH2", + degeneracy = 1, + kinetics = Arrhenius(A=(3.14e+07, 'cm^3/(mol*s)'), n=1.77, Ea=(3729, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R18: beta scission""", +) + +entry( + index = 19, + label = "C2H4 + NH2 <=> CH2CH2NH2", + degeneracy = 1, + kinetics = Arrhenius(A=(1.23e+03, 'cm^3/(mol*s)'), n=2.76, Ea=(1658, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R19: beta scission""", +) + +entry( + index = 20, + label = "CH3CHNH2 <=> CH2CHNH2 + H", + degeneracy = 1, + kinetics = Arrhenius(A=(1.14e+09, 's^-1'), n=1.49, Ea=(35100, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R20: beta scission""", +) + +entry( + index = 21, + label = "CH2NH + H <=> CH2NH2", + degeneracy = 1, + kinetics = Arrhenius(A=(1.48e+08, 'cm^3/(mol*s)'), n=1.67, Ea=(2.295, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R21: beta scission""", +) + +entry( + index = 22, + label = "CH2CHNH <=> CH2CNH + H", + degeneracy = 1, + kinetics = Arrhenius(A=(2.18e+07, 's^-1'), n=2.26, Ea=(50300, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R22: beta scission""", +) + +entry( + index = 23, + label = "CH3CHN <=> CH3 + HCN", + degeneracy = 1, + kinetics = Arrhenius(A=(7.52e+10, 's^-1'), n=1.10, Ea=(26200, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R23: beta scission""", +) + +entry( + index = 24, + label = "CH3CHN <=> CH3CN + H", + degeneracy = 1, + kinetics = Arrhenius(A=(1.49e+09, 's^-1'), n=1.44, Ea=(27000, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R24: beta scission""", +) + +entry( + index = 25, + label = "CH2CH2NH2 <=> CH3CHNH2", + degeneracy = 1, + kinetics = Arrhenius(A=(3.12e+04, 's^-1'), n=2.33, Ea=(31800, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R25: intra H transfer""", +) + +entry( + index = 26, + label = "CH2CHNH <=> CH3CHN", + degeneracy = 1, + kinetics = Arrhenius(A=(9.20e+05, 's^-1'), n=2.16, Ea=(37400, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R26: intra H transfer""", +) + +entry( + index = 27, + label = "NCC <=> C2H4 + NH3", + degeneracy = 1, + kinetics = Arrhenius(A=(4.90e+04, 's^-1'), n=2.65, Ea=(65100, 'cal/mol'), T0=(1, 'K')), + shortDesc = u"""Table 2, R27: 1,2-elimination""", +) +