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ReactionMechanismGenerator / RMG-database

The database of chemical parameters used with Reaction Mechanism Generator
http://rmg.mit.edu/database/
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Removed database entries #133

Open nyee opened 7 years ago

nyee commented 7 years ago

I'm writing this issue as a place to store entries removed from RMG-database. Sometimes changes in code or questionable sources may make us want to remove some (hopefully temporarily). Putting them here, prevents them from being lost forever, especially if they are unpublished or unrecorded elsewhere.

The following entry was removed because we recently changed out Nitrogen atomtypes to be more specific. Previously it was 'swept under the rug', probably falling under some atomtype that was not intended. In the current working version of NAtomType branch, there is no atomtype to describe the negative 2 charged nitrogen:

from thermo_DFT_CCSDTF12_BAC thermo library:

~~entry( index = 434, label = "NNH2(S)", molecule = """ 1 N u0 p0 c+2 {2,S} {3,S} {4,S} 2 H u0 p0 c0 {1,S} 3 H u0 p0 c0 {1,S} 4 N u0 p3 c-2 {1,S} """, thermo = ThermoData( Tdata = ([300,400,500,600,800,1000,1500],'K'), Cpdata = ([8.61,9.45,10.46,11.48,13.24,14.63,16.86],'cal/(molK)'), H298 = (71.66,'kcal/mol'), S298 = (52.09,'cal/(molK)'), ), shortDesc = u"""""", longDesc = u""" level of theory: CCSD(T)F12A/cc-pVTZ-F12//B3LYP/6-311++g(d,p) + BAC """, )~~

Edit: The above entry is now re-implemented with #163.

nyee commented 7 years ago

The following entries were removed because RMG cannot currently process reactions with more than 3 products or reactants:

From JetSurF2.0 kinetics library:

entry(
   index = 718,
   label = "C6H4O2 + O <=> CO + CO + C2H2 + CH2CO",
   degeneracy = 1,
   kinetics = Arrhenius(
       A = (3e+13, 'cm^3/(mol*s)'),
       n = 0,
       Ea = (5000, 'cal/mol'),
       T0 = (1, 'K'),
       comment = 'est. HW k = kinf[C6H6 + H]',
   ),
   longDesc = 
u"""
est. HW k = kinf[C6H6 + H]
""",
)

entry(
   index = 1440,
   label = "OC12OOH <=> CH2O + C2H4 + C2H4 + C2H4 + C2H4 + C2H5 + OH + CO",
   degeneracy = 1,
   kinetics = Arrhenius(A=(7e+14, 's^-1'), n=0, Ea=(42065, 'cal/mol'), T0=(1, 'K')),
)

From CurranPentane:

entry(
    index = 705,
    label = "CY(CCOC)OH + OH => CH2O + CH2CO + H + H2O",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(2260, 'cm^3/(mol*s)'), n=2.73, Ea=(-4688, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 710,
    label = "CY(CCOC)OH + HO2 => CH2O + CH2CO + H + H2O2",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(8.6, 'cm^3/(mol*s)'), n=3.46, Ea=(9732.33, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 728,
    label = "OHCOCOOHCH3 => CO + CH3CHO + OH + OH",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(1.59e+20, 's^-1'), n=-1.5, Ea=(42879.5, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 735,
    label = "CHOCOHCH2OOH => OH + CH2O + H + CHOCHO",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(1.59e+20, 's^-1'), n=-1.5, Ea=(42879.5, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 1735,
    label = "P-C6H3O2 + H <=> C2H2 + C2H2 + CO + CO",
    degeneracy = 1,
    kinetics = Arrhenius(A=(1e+14, 'cm^3/(mol*s)'), n=0, Ea=(0, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 1736,
    label = "P-C6H3O2 + O => C2H2 + HCCO + CO + CO",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(1e+14, 'cm^3/(mol*s)'), n=0, Ea=(0, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

RMG does not accept reactions with more than 3 products in its solver
entry(
    index = 1737,
    label = "P-C6H4O2 + O => CO + CO + C2H2 + CH2CO",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(3e+13, 'cm^3/(mol*s)'), n=0, Ea=(5000, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 1953,
    label = "CH2CQCOHQ => HOCHO + CH2CO + OH + OH",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(1.59e+20, 's^-1'), n=-1.5, Ea=(42879.5, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 1954,
    label = "CH2CQCOHQ => HCO + CH2CO + OH + OH + OH",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(1.59e+20, 's^-1'), n=-1.5, Ea=(42879.5, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 1956,
    label = "COHQCYC(COC) => HOCHO + CH2O + C2H3 + OH",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(1.59e+20, 's^-1'), n=-1.5, Ea=(42879.5, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 1957,
    label = "QCYC(CCOC)OH => HOCHO + CH2CO + CH3 + OH",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(1.59e+20, 's^-1'), n=-1.5, Ea=(42879.5, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 1960,
    label = "HOCOCQ(CH3)2 => CO + CH3COCH3 + OH + OH",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(1.59e+20, 's^-1'), n=-1.5, Ea=(42879.5, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 1963,
    label = "CH2COHCH2OOH => OH + CH2O + CH2CO + H",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(1.59e+20, 's^-1'), n=-1.5, Ea=(42879.5, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 1965,
    label = "CH2C(CH2OOH)2 => OH + CH2O + HO2 + C3H4-A",
    degeneracy = 1,
    duplicate = True,
    reversible = False,
    kinetics = MultiArrhenius(
        arrhenius = [
            Arrhenius(A=(1.59e+20, 's^-1'), n=-1.5, Ea=(42879.5, 'cal/mol'), T0=(1, 'K')),
            Arrhenius(A=(1e+16, 's^-1'), n=0, Ea=(43000, 'cal/mol'), T0=(1, 'K')),
        ],
    ),
    shortDesc = u"""""",
)

entry(
    index = 1968,
    label = "C3KET21 => OH + CH2O + CO + CH3",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(1.59e+20, 's^-1'), n=-1.5, Ea=(42879.5, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 1970,
    label = "CO(CH2OOH)2 => OH + OH + CH2O + CH2O + CO",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(1.59e+20, 's^-1'), n=-1.5, Ea=(42879.5, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 1972,
    label = "CHOC(CH3)OHCH2Q => OH + CH2O + H + CH3COCHO",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(1.59e+20, 's^-1'), n=-1.5, Ea=(42879.5, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

entry(
    index = 1973,
    label = "CH3COCHO + OH => CO + CO + CH3 + H2O",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(
        A = (61329.9, 'cm^3/(mol*s)'),
        n = 2.65419,
        Ea = (-4586.4, 'cal/mol'),
        T0 = (1, 'K'),
    ),
    shortDesc = u"""""",
)

entry(
    index = 3083,
    label = "NEOC5H9O-OOH => C3H5-T + CH2O + CH2O + OH",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(A=(1e+16, 's^-1'), n=0, Ea=(43000, 'cal/mol'), T0=(1, 'K')),
    shortDesc = u"""""",
)

From Klippenstein_Glarborg2016:

entry(
    index = 281,
    label = "C2H2 + O2 <=> H + CO + H + CO",
    degeneracy = 1,
    duplicate = True,
    kinetics = MultiArrhenius(
        arrhenius = [
            Arrhenius(
                A = (6.094e+26, 'cm^3/(mol*s)'),
                n = -3.276,
                Ea = (110815, 'cal/mol'),
                T0 = (1, 'K'),
            ),
            Arrhenius(
                A = (2.185e+32, 'cm^3/(mol*s)'),
                n = -4.946,
                Ea = (93104.6, 'cal/mol'),
                T0 = (1, 'K'),
            ),
        ],
    ),
    shortDesc = u"""The chemkin file reaction is C2H2 + O2 <=> H + CO + H + CO""",
)

entry(
    index = 392,
    label = "CH2CHOH + O2 => CH2O + H + CO + OH",
    degeneracy = 1,
    reversible = False,
    kinetics = Arrhenius(
        A = (2.095e+17, 'cm^3/(mol*s)'),
        n = -0.673,
        Ea = (58927.3, 'cal/mol'),
        T0 = (1, 'K'),
    ),
    shortDesc = u"""The chemkin file reaction is CH2CHOH + O2 => CH2O + H + CO + OH""",
)

entry(
    index = 464,
    label = "HCCO + O2 <=> H + CO + CO + O",
    degeneracy = 1,
    kinetics = Arrhenius(
        A = (1.317e+12, 'cm^3/(mol*s)'),
        n = 0.217,
        Ea = (23467.3, 'cal/mol'),
        T0 = (1, 'K'),
    ),
    shortDesc = u"""The chemkin file reaction is HCCO + O2 <=> H + CO + CO + O""",
)
nyee commented 7 years ago

The following removed entries are from three libraries relating to sulfur. @mliu49 says these were also commented out in @cclass86's RMG-Java libraries. We are not sure why they were commented out.

From Hexenethiel_nr library: 

#entry(
#    index = 1,
#    label = "C6H12SHOH <=> C6H12O + H2S",
#    degeneracy = 1,
#    kinetics = Arrhenius(A=(3.43e+14, 's^-1'), n=-0.41, Ea=(44.42, 'kcal/mol'), T0=(1, 'K')),
#    longDesc = 
#u"""
#First one should be 36.30 kcal/mol, second 44.42 kcal/mol
#C6H12O + H2S = C6H12SHOH    6.13E+01    2.77    36.30    0.0    0.0    0.0
#""",
#)
#
#entry(
#    index = 3,
#    label = "C5H11J + COS <=> C5H11COSJ",
#    degeneracy = 1,
#    kinetics = Arrhenius(
#        A = (8.02E+06, 'cm^3/(mol*s)'),
#        n = 1.68,
#        Ea = (12.09, 'kcal/mol'),
#        T0 = (1, 'K'),
#    ),
#)
#
#entry(
#    index = 4,
#    label = "CHOHS + C5H11J <=> C6H12OHSJ",
#    degeneracy = 1,
#    kinetics = Arrhenius(A=(760, 'cm^3/(mol*s)'), n=2.56, Ea=(3.56, 'kcal/mol'), T0=(1, 'K')),
#)
#
#entry(
#    index = 5,
#    label = "C4H9CHJCHOHSH <=> SH + hexen-1-ol",
#    degeneracy = 1,
#    kinetics = Arrhenius(A=(1.92e+12, 's^-1'), n=0.14, Ea=(5.35, 'kcal/mol'), T0=(1, 'K')),
#    longDesc = 
#u"""
#reverse of reaction is in R_Addition_MultipleBond library:
#""",
#)

#entry(
#    index = 6,
#    label = "hexen-1-ol <=> C6H12O",
#    degeneracy = 1,
#    kinetics = Arrhenius(A=(5.32e-33, 's^-1'), n=12.94, Ea=(31.33, 'kcal/mol'), T0=(1, 'K')),
#)
#
#entry(
#    index = 7,
#    label = "CO + H2O <=> CO2 + H2",
#    degeneracy = 1,
#    kinetics = Arrhenius(A=(5000, 'cm^3/(mol*s)'), n=0, Ea=(0, 'kcal/mol'), T0=(1, 'K')),
#    longDesc = 
#u"""
#Approx water gas shift reaction
#""",
#)

From Thial_Hydrolysis:

#entry(
#    index = 1,
#    label = "CH2S + H2O <=> CH2OHSH",
#    degeneracy = 1,
#    kinetics = Arrhenius(A=(960, 'cm^3/(mol*s)'), n=2.43, Ea=(28.13, 'kcal/mol'), T0=(1, 'K')),
#)
#
#entry(
#    index = 2,
#    label = "CH3CHS + H2O <=> CHCH3OHSH",
#    degeneracy = 1,
#    kinetics = Arrhenius(A=(15.4, 'cm^3/(mol*s)'), n=2.78, Ea=(27.8, 'kcal/mol'), T0=(1, 'K')),
#)
#

From Sendt

#entry(
#    index = 5,
#    label = "H + HSS <=> SH + SH",
#    degeneracy = 1,
#    kinetics = Arrhenius(
#        A = (1.1e+13, 'cm^3/(mol*s)'),
#        n = 0.353,
#        Ea = (0.21, 'kcal/mol'),
#        T0 = (1, 'K'),
#    ),
#    longDesc = 
# u"""
# Using unadjusted singlet surface calculation for this one (see paper)
# """,
#)
nyee commented 7 years ago

The following entries were removed until we implement hypervalent sulfur

From solvation/abraham.py

# entry(
#     index = 35,
#     label = "SdsOsOdOd",
#     group = 
# """
# 1 * Sd u0 {2,D} {3,D} {4,S} {5,S}
# 2   Od u0 {1,D}
# 3   Od u0 {1,D}
# 4   Os u0 {1,S}
# 5   R  u0 {1,S}
# """,
#     solute = SoluteData(
#         S = -0.505,
#         B = -0.188,
#         E = 0.0,
#         L = 0.0,
#         A = 0.0,
#     ),
#     shortDesc = u"""Platts fragment 35 sulfonate""",
#     longDesc = 
# u"""

# """,
# )

From solvation/nonacentered.py

# entry(
#     index = 26,
#     label = "SdOdOdN",
#     group = 
# """
# 1 * Sd u0 {2,D} {3,D} {4,S}
# 2   Od u0 {1,D}
# 3   Od u0 {1,D}
# 4   N  u0 {1,S}
# """,
#     solute = SoluteData(
#         S = -0.569,
#         B = -0.446,
#         E = -0.111,
#         L = 0.0,
#         A = 0.356,
#     ),
#     shortDesc = u"""Platts group 51 sulfonamide -S(O)(O)N- (and fragment 13 for A)""",
#     longDesc = 
# u"""

# """,
# )
nyee commented 7 years ago

These entries were removed because we cannot handle S4b atomtype, and more generally 5-ring aromatics:

from solvation/abraham.py

# entry(
#     index = 32,
#     label = "Ss-aromatic",
#     group = 
# """
# 1 * S4b      u0 {2,B} {5,B}
# 2   Cb       u0 {1,B} {3,B}
# 3   [Cb,N3b] u0 {2,B} {4,B}
# 4   [Cb,N3b] u0 {3,B} {5,B}
# 5   Cb       u0 {1,B} {4,B}
# """,
#     solute = SoluteData(
#         S = 0,
#         B = 0.043,
#         E = 0.116,
#         L = 0.848,
#         A = 0,
#     ),
#     shortDesc = u"""Platts fragment 32 -S- aromatic""",
#     longDesc = 
# u"""

# """,
# )
nyee commented 6 years ago

From H-abstraction rules: This rule calculates rates more than 10 orders of magnitude lower than anything else in the family. @alongd and I were not able to find it in the stated reference even after an hour of searching. 

entry(
    index = 2007,
    label = "C/H3/Cs;InChI=1S/NO3/c2-1(3)4",
    kinetics = ArrheniusEP(
        A = (2.03e-12, 'cm^3/(mol*s)'),
        n = 0,
        alpha = 0,
        E0 = (8.31, 'kcal/mol'),
        Tmin = (300, 'K'),
        Tmax = (2000, 'K'),
    ),
    rank = 1,
    shortDesc = u"""Added by Beat Buesser from 'Gas-Phase Combustion Chemistry' (ISBN: 978-1-4612-7088-1), chapter 2, 'Combustion Chemistry of Nitrogen', Anthony M. Dean, Joseph W. Bozzelli""",
)
alongd commented 6 years ago

From the SOxNOx kinetic library: some reactions by Lin2014b seem to have an unreasonable rate. For example, the rate of N2H4 <=> NH2 + NH2 by [Lin2014b] is about O(20) lower than the rate by [Klippenstein2009]. All reactions from this source were commented out until this is further investigated. Given here for documentation in case they get deleted in the future:

[Lin2014b] P. Raghunath, N.T. Nghia, M.C. Lin, Advances in Quantum Chemistry, 2014, 69, 253-301, doi: 10.1016/B978-0-12-800345-9.00007-6

entry(
    index = 99,
    label = "N2H4 <=> NH2 + NH2",
    degeneracy = 1,
    kinetics = Arrhenius(A=(1.57e+21, 's^-1'), n=-1.04, Ea=(66565, 'cal/mol'), T0=(1, 'K'), Tmin=(700, 'K'), Tmax=(2000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 264
T range: 700-2000 K
calculations done at the RCCSD(T)/6-311þG(3df,2p)//B3LYP/6-311G(d,p) level of theoty
Only High Pressure Limit rate was taken; low limit and 1 atm rate are also available from the same source
Also available from [Klippenstein2009]:
    kinetics = Troe(
        arrheniusHigh = Arrhenius(A=(9.33e-10, 's^-1'), n=-0.414, Ea=(33, 'cal/mol'), T0=(1, 'K')),
        arrheniusLow = Arrhenius(A=(4.48e-14, 'cm^3/(mol*s)'), n=-5.49, Ea=(1000, 'cal/mol'), T0=(1, 'K')),
        alpha=0.31, T3=(1e-30, 'K'), T1=(1e+30, 'K'), efficiencies={}),
Table 3, p. 10245, T range: 300-2500 K, calculated at the (CCSD(T) and CAS+1+2+QC level
Added as a training reaction to R_Recombination
""",
)

entry(
    index = 100,
    label = "N2H4 <=> N2H3 + H",
    degeneracy = 1,
    kinetics = Arrhenius(A=(5.69e+14, 's^-1'), n=-0.28, Ea=(76678, 'cal/mol'), T0=(1, 'K'), Tmin=(700, 'K'), Tmax=(2000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 264
T range: 700-2000 K
calculations done at the RCCSD(T)/6-311þG(3df,2p)//B3LYP/6-311G(d,p) level of theoty
Only High Pressure Limit rate was taken low limit and 1 atm rate are also available from the same source
Added as a training reaction to R_Recombination
""",
)

entry(
    index = 101,
    label = "ONONO2 <=> NO2 + NO2",
    degeneracy = 1,
    kinetics = Arrhenius(A=(1.69e+23, 's^-1'), n=-2.43, Ea=(8148, 'cal/mol'), T0=(1, 'K'), Tmin=(700, 'K'), Tmax=(2000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 265
T range: 700-2000 K
calculations done at the UCCSD(T)/CBS//UB3LYP/6-311þþG(3df,2p) level of theoty
Only High Pressure Limit rate was taken low limit and 1 atm rate are also available from the same source
""",
)

entry(
    index = 102,
    label = "ONONO2 <=> NO + NO3",
    degeneracy = 1,
    kinetics = Arrhenius(A=(2.41e+21, 's^-1'), n=-1.76, Ea=(31535, 'cal/mol'), T0=(1, 'K'), Tmin=(700, 'K'), Tmax=(2000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 265
T range: 700-2000 K
calculations done at the UCCSD(T)/CBS//UB3LYP/6-311þþG(3df,2p) level of theoty
Only High Pressure Limit rate was taken low limit and 1 atm rate are also available from the same source
Added as a training reaction to R_Recombination
""",
)

entry(
    index = 103,
    label = "N2H4 + NO2 <=> N2H3 + HONO",
    degeneracy = 1,
    kinetics = Arrhenius(A=(3.23e+00, 'cm^3/(mol*s)'), n=3.56, Ea=(763, 'cal/mol'), T0=(1, 'K'), Tmin=(250, 'K'), Tmax=(2500, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 265
T range: 250-2500 K
calculations done at the G2M(CC2)//B3LYP/6-311þþG(3df,2p) level of theoty
Also available from [Lin2014a], calculated at the CCSD(T)/CBS//CCSD level of theoty:
    kinetics = Arrhenius(A=(8.25e+01, 'cm^3/(mol*s)'), n=3.13, Ea=(8863, 'cal/mol'), T0=(1, 'K')),
Added as a training reaction to H_Abstraction
""",
)

entry(
    index = 104,
    label = "N2H4 + NO3 <=> N2H3 + HNO3",
    degeneracy = 1,
    kinetics = Arrhenius(A=(1.28e+04, 'cm^3/(mol*s)'), n=2.53, Ea=(-2947, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(3000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 269
T range: 300-3000 K
calculations done at the CCSD(T)//BHandHLYP/6-311þþG(3df,2p) level of theoty
Pressure independent at least up to 100 atm
A different rate for the same reaction is available from the same author (M.C. Lin) published in the same year...: [Lin2014a]
But this [Lin2014a] rate is a factor of 3 lower at 1500 K:
    kinetics = Arrhenius(A=(6.20e+03, 'cm^3/(mol*s)'), n=2.64, Ea=(594, 'cal/mol'), T0=(1, 'K')),
[Lin2014a] reaction (6), p. 79
T range: 300-2000 K
calculations done at the CCSD(T)/CBS//CCSD level of theoty,
and the moment of inertia and harmonic vibrational frequencies were obtained by the CCSD/6-31G(d,p) level
Added as a training reaction to H_Abstraction
""",
)

entry(
    index = 105,
    label = "N2H4 + NO3 <=> HONO + N2H3O",
    degeneracy = 1,
    kinetics = Arrhenius(A=(3.46e+03, 'cm^3/(mol*s)'), n=2.51, Ea=(-7452, 'cal/mol'), T0=(1, 'K'), Tmin=(1000, 'K'), Tmax=(3000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 269
T range: 1000-3000 K
calculations done at the CCSD(T)//BHandHLYP/6-311þþG(3df,2p) level of theoty
Pressure independent at least up to 100 atm
The Low T (300-1000 K) rate is:
    kinetics = Arrhenius(A=(1.10e+18, 'cm^3/(mol*s)'), n=-1.84, Ea=(-642, 'cal/mol'), T0=(1, 'K')),
A different rate for the same reaction is available from the same author (M.C. Lin) published at the same year: [Lin2014a]
But this [Lin2014a] rate is a O(2) lower at 1500 K:
    kinetics = Arrhenius(A=(2.04e+03, 'cm^3/(mol*s)'), n=2.59, Ea=(5612, 'cal/mol'), T0=(1, 'K')),
T range: 1000-2000 K
    kinetics = Arrhenius(A=(1.63e+11, 'cm^3/(mol*s)'), n=0.20, Ea=(2180, 'cal/mol'), T0=(1, 'K')),
T range: 300-1000 K
[Lin2014a] reaction (7), p. 79
calculations done at the CCSD(T)/CBS//CCSD level of theoty,
and the moment of inertia and harmonic vibrational frequencies were obtained by the CCSD/6-31G(d,p) level
""",
)

entry(
    index = 106,
    label = "N2H4 + N2O4 <=> HONO + NH2NHNO2",
    degeneracy = 1,
    kinetics = Arrhenius(A=(1.39e+02, 'cm^3/(mol*s)'), n=2.62, Ea=(13112, 'cal/mol'), T0=(1, 'K'), Tmin=(200, 'K'), Tmax=(2500, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 271
T range: 200-2500 K
calculations done at the G2M(CC3)//B3LYP level of theoty
""",
)

entry(
    index = 107,
    label = "N2H4 + ONONO2 <=> HNO3 + NH2NHNO",
    degeneracy = 1,
    kinetics = Arrhenius(A=(4.7e+14, 'cm^3/(mol*s)','+|-',6.1e+13), n=0, Ea=(0, 'cal/mol'), T0=(1, 'K'), Tmin=(250, 'K'), Tmax=(2500, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 272
T range: 250-2500 K
calculations done at the G2M(CC3)//B3LYP level of theoty
Reaction has a negligible T dependence in the explored range
uncertainty: +/- 13%
conformer-dup: The T-dependency of both cis-ONONO2 and trans-ONONO2 reacting with N2H4
in this pathway is negligable. The summation of the two constant rate coefficients is taken here.
""",
)

entry(
    index = 108,
    label = "NH2NHNO <=> N2H3 + NO",
    degeneracy = 1,
    kinetics = Arrhenius(A=(6.24e+15, 's^-1'), n=-0.15, Ea=(35611, 'cal/mol'), T0=(1, 'K'), Tmin=(250, 'K'), Tmax=(1500, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 274
T range: 250-1500 K
calculations done at the CCSD(T)/6-311þG(3df,2p) level of theoty
Added as a training reaction to R_Recombination
""",
)

entry(
    index = 109,
    label = "N2H3 + NO2 <=> N2H2 + HONO",
    degeneracy = 1,
    kinetics = Arrhenius(A=(2.40e+55, 'cm^3/(mol*s)'), n=-16.7, Ea=(-14397, 'cal/mol'), T0=(1, 'K'), Tmin=(800, 'K'), Tmax=(3000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
k5, p. 278
T range: 800-3000 K, P = 1 atm
calculations done at the CCSD(T)/6-311++G(3df,2p)//B3LYP/6-311++G(3df,2p) level of theoty
The Low T (300-800 K) rate is:
    kinetics = Arrhenius(A=(4.99e+46, 'cm^3/(mol*s)'), n=-11.8, Ea=(6055, 'cal/mol'), T0=(1, 'K')),
Added as a training reaction to Disproportionation
""",
)

entry(
    index = 110,
    label = "N2H3 + NO2 <=> N2H2 + HNO2",
    degeneracy = 1,
    kinetics = Arrhenius(A=(5.12e+07, 'cm^3/(mol*s)'), n=-0.2, Ea=(-2736, 'cal/mol'), T0=(1, 'K'), Tmin=(1500, 'K'), Tmax=(3000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
k7 p. 278
T range: 1500-3000 K, P = 1 atm
calculations done at the CCSD(T)/6-311++G(3df,2p)//B3LYP/6-311++G(3df,2p) level of theoty
The Low T (300-1500 K) rate is:
    kinetics = Arrhenius(A=(4.07e+08, 'cm^3/(mol*s)'), n=0.5, Ea=(-2395, 'cal/mol'), T0=(1, 'K')),
""",
)

entry(
    index = 111,
    label = "N2H3 + NO2 <=> N2H3O + NO",
    degeneracy = 1,
    kinetics = Arrhenius(A=(6.14e+00, 'cm^3/(mol*s)'), n=2.8, Ea=(-8853, 'cal/mol'), T0=(1, 'K'), Tmin=(1000, 'K'), Tmax=(3000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
k6, p. 278
T range: 1000-3000 K, P = 1 atm
calculations done at the CCSD(T)/6-311++G(3df,2p)//B3LYP/6-311++G(3df,2p) level of theoty
The Low T (300-1000 K) rate is:
    kinetics = Arrhenius(A=(1.08e+20, 'cm^3/(mol*s)'), n=-2.9, Ea=(792.3, 'cal/mol'), T0=(1, 'K')),
""",
)

entry(
    index = 112,
    label = "N2H3 + N2O4 <=> NH2NHNO2 + NO2",
    degeneracy = 1,
    kinetics = Arrhenius(A=(1.10e+10, 'cm^3/(mol*s)'), n=0.87, Ea=(11772, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(3000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 281
T range: 300-3000 K
calculations done at the CCSD(T)/6-311þþG(3df,2p)//B3LYP/6-311þþG(3df,2p) level of theoty
""",
)

entry(
    index = 113,
    label = "N2H3 + N2O4 <=> N2H2 + HONO + NO2",
    degeneracy = 1,
    kinetics = Arrhenius(A=(8.55e+10, 'cm^3/(mol*s)'), n=0.74, Ea=(11707, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(3000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 281
T range: 300-3000 K
calculations done at the CCSD(T)/6-311þþG(3df,2p)//B3LYP/6-311þþG(3df,2p) level of theoty
""",
)

entry(
    index = 114,
    label = "N2H3 + N2O4 <=> NH2NHONO + NO2",
    degeneracy = 1,
    kinetics = Arrhenius(A=(4.54e+13, 'cm^3/(mol*s)'), n=0.76, Ea=(15960, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(3000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 281
T range: 300-3000 K
calculations done at the CCSD(T)/6-311þþG(3df,2p)//B3LYP/6-311þþG(3df,2p) level of theoty
""",
)

entry(
    index = 115,
    label = "N2H3 + N2O4 <=> N2H3O + N2O3",
    degeneracy = 1,
    kinetics = Arrhenius(A=(3.69e+11, 'cm^3/(mol*s)'), n=0.87, Ea=(8047.4, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(3000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 281
T range: 300-3000 K
calculations done at the CCSD(T)/6-311þþG(3df,2p)//B3LYP/6-311þþG(3df,2p) level of theoty
""",
)

entry(
    index = 116,
    label = "N2H3O <=> NH3 + NO",
    degeneracy = 1,
    kinetics = Arrhenius(A=(2.86e+22, 's^-1'), n=-2.80, Ea=(79296, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(3000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 284
T range: 300-3000 K, P = 1 atm
calculations done at the CCSD(T)/6-311þG(3df,2p)//CCSD/6-311þþG(d,p) level of theoty
""",
)

entry(
    index = 117,
    label = "N2H3O <=> NH2 + HNO",
    degeneracy = 1,
    kinetics = Arrhenius(A=(9.12e+33, 's^-1'), n=-6.68, Ea=(35217, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(3000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 284
T range: 300-3000 K, P = 1 atm
calculations done at the CCSD(T)/6-311þG(3df,2p)//CCSD/6-311þþG(d,p) level of theoty
Added as a training reaction to R_Additiom_MultipleBond
""",
)

entry(
    index = 118,
    label = "N2H3O <=> NH2NO + H",
    degeneracy = 1,
    kinetics = Arrhenius(A=(1.57e+34, 's^-1'), n=-6.63, Ea=(44953, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(3000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 284
T range: 300-3000 K, P = 1 atm
calculations done at the CCSD(T)/6-311þG(3df,2p)//CCSD/6-311þþG(d,p) level of theoty
Added as a training reaction to R_Additiom_MultipleBond
""",
)

entry(
    index = 119,
    label = "N2H2 + NO2 <=> HONO + NNH",
    degeneracy = 1,
    kinetics = MultiArrhenius(
        arrhenius = [
            Arrhenius(A=(1.25e+00, 'cm^3/(mol*s)'), n=3.80, Ea=(10410, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(2500, 'K')),
            Arrhenius(A=(2.33e-01, 'cm^3/(mol*s)'), n=3.50, Ea=(-129, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(2500, 'K')),
        ],
    ),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 287
T range: 300-2500 K
calculations done at the CCSD(T)/6-311þþG(3df,2p)//B3LYP/6-311þþG(3df,2p) level of theoty
conformer-dup: rates summed for trans/cis-N2H2
""",
)

entry(
    index = 120,
    label = "N2H2 + N2O4 <=> HONO + NO2 + NNH",
    degeneracy = 1,
    kinetics = Arrhenius(A=(8.79e+00, 'cm^3/(mol*s)'), n=3.10, Ea=(28787, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(2500, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 288
T range: 300-2500 K
calculations done at the B3LYP/6-311þþG(3df,2p) level
""",
)

entry(
    index = 121,
    label = "N2H2 + N2O4 <=> HONO + HNO2 + N2",
    degeneracy = 1,
    kinetics = Arrhenius(A=(2.38e-02, 'cm^3/(mol*s)'), n=3.90, Ea=(13360, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(2500, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 288
T range: 300-2500 K
calculations done at the B3LYP/6-311þþG(3df,2p) level
""",
)

entry(
    index = 122,
    label = "N2H2 + OH <=> NNH + H2O",
    degeneracy = 1,
    kinetics = MultiArrhenius(
        arrhenius = [
            Arrhenius(A=(6.74e+03, 'cm^3/(mol*s)'), n=2.80, Ea=(-507, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(2500, 'K')),
            Arrhenius(A=(7.65e+04, 'cm^3/(mol*s)'), n=2.25, Ea=(-2351, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(2500, 'K')),
        ],
    ),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 292
T range: 300-2500 K
calculations done at the CCSD(T)/6-311++G(3df,2p)//B3LYP/6311++G(3df,2p) level of theory
conformer-dup: rates summed for trans/cis-N2H2
""",
)

Also deleted for the same reason from the SOxNOx/LowT library:

entry(
    index = 105,
    label = "N2H4 + NO3 <=> HONO + N2H3O",
    degeneracy = 1,
    kinetics = Arrhenius(A=(1.10e+18, 'cm^3/(mol*s)'), n=-1.84, Ea=(-642, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(1000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
p. 269
T range: 300-1000 K (also available at 1000-3000 K)
calculations done at the CCSD(T)//BHandHLYP/6-311þþG(3df,2p) level of theoty
Pressure independent at least up to 100 atm
A different rate for the same reaction is available from the same author (M.C. Lin) published in the same year...: [Lin2014a]
But this [Lin2014a] rate is a O(2) lower at 1500 K:
    kinetics = Arrhenius(A=(2.04e+03, 'cm^3/(mol*s)'), n=2.59, Ea=(5612, 'cal/mol'), T0=(1, 'K')),
T range: 1000-2000 K
    kinetics = Arrhenius(A=(1.63e+11, 'cm^3/(mol*s)'), n=0.20, Ea=(2180, 'cal/mol'), T0=(1, 'K')),
T range: 300-1000 K
[Lin2014a] reaction (7), p. 79
calculations done at the CCSD(T)/CBS//CCSD level of theoty,
and the moment of inertia and harmonic vibrational frequencies were obtained by the CCSD/6-31G(d,p) level
""",
)

entry(
    index = 109,
    label = "N2H3 + NO2 <=> N2H2 + HONO",
    degeneracy = 1,
    kinetics = Arrhenius(A=(4.99e+46, 'cm^3/(mol*s)'), n=-11.8, Ea=(6055, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(800, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
k5, p. 278
T range: 300-800 K (also available at 800-3000 K), P = 1 atm
calculations done at the CCSD(T)/6-311++G(3df,2p)//B3LYP/6-311++G(3df,2p) level of theoty
""",
)

entry(
    index = 110,
    label = "N2H3 + NO2 <=> N2H2 + HNO2",
    degeneracy = 1,
    kinetics = Arrhenius(A=(4.07e+08, 'cm^3/(mol*s)'), n=0.5, Ea=(-2395, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(1500, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
k7 p. 278
T range: 300-1500 K (also available at 1500-3000 K), P = 1 atm
calculations done at the CCSD(T)/6-311++G(3df,2p)//B3LYP/6-311++G(3df,2p) level of theoty
""",
)

entry(
    index = 111,
    label = "N2H3 + NO2 <=> N2H3O + NO",
    degeneracy = 1,
    kinetics = Arrhenius(A=(1.08e+20, 'cm^3/(mol*s)'), n=-2.9, Ea=(792.3, 'cal/mol'), T0=(1, 'K'), Tmin=(300, 'K'), Tmax=(1000, 'K')),
    shortDesc = u"""[Lin2014b]""",
    longDesc =
u"""
Part of the "N2H4 + N2O4" subset
k6, p. 278
T range: 300-1000 K (also available at 1000-3000 K), P = 1 atm
calculations done at the CCSD(T)/6-311++G(3df,2p)//B3LYP/6-311++G(3df,2p) level of theoty
""",
)
alongd commented 6 years ago

The OxygenSingTrip library was deleted in #239:

name = "OxygenSingTrip"
shortDesc = u"reactions of singlet and triplet oxygen"
longDesc = u"""
Reactions of singlet and triplet oxygen. added based on the new adjacency list representation in 2014 by Connie
"""
entry(
    index = 1,
    label = "O2S => O2",
    degeneracy = 1,
    duplicate = True,
    reversible = False,
    kinetics = Arrhenius(A=(0.00023, 's^-1'), n=0, Ea=(0, 'kJ/mol'), T0=(1, 'K')),
)

entry(
    index = 2,
    label = "O2S => O2",
    degeneracy = 1,
    duplicate = True,
    reversible = False,
    kinetics = ThirdBody(
        arrheniusLow = Arrhenius(A=(4.05, 'cm^3/(mol*s)'), n=0, Ea=(0, 'kJ/mol'), T0=(1, 'K')),
        efficiencies = {'[O][O]': 5.43, 'O=C=O': 4.29},
    ),
)

entry(
    index = 3,
    label = "O2S <=> O2",
    degeneracy = 1,
    duplicate = True,
    kinetics = ThirdBody(
        arrheniusLow = Arrhenius(A=(3e+06, 'cm^3/(mol*s)'), n=0, Ea=(0, 'kJ/mol'), T0=(1, 'K')),
        efficiencies = {'c1ccccc1': 1.067, 'O': 1.783, '[H][H]': 1, '[O][O]': 0.34, 'N#N': 0.028, '[C]=O': 14, '[Ar]': 0.00166},
    ),
)
O2S
1 O u0 p2 c0 {2,D}
2 O u0 p2 c0 {1,D}

O2
multiplicity 3
1 O u1 p2 c0 {2,S}
2 O u1 p2 c0 {1,S}
mjohnson541 commented 6 years ago

Removed in #280 from Birad_R_Recombination training 

This is commented out because currently GAV can't estimate the reverse rate
which results in rates that are many orders of magnitude faster than they should
be, when this is no longer a problem for these species, this can be uncommented
entry(
   index = 3,
   label = "HSOO <=> HSO + O",
   degeneracy = 1,
   kinetics = Arrhenius(A=(2.01e+19, 's^-1'), n=-1.07, Ea=(28377, 'cal/mol'), T0=(1, 'K'), Tmin = (200, 'K'), Tmax = (2000, 'K')),
   rank = 2,
   shortDesc = u"""Training reaction from kinetics library: primarySulfurLibrary""",
   longDesc =
u"""
T range: 200-2000 K
A. Goumri, J-D.R. Rocha, D. Laakso, C.E. Smith, P. Marshall, J. Phys. Chem. A, 1999, 103(51), 11328-11335 doi: 10.1021/jp9924070
Table 7 on p. 11333
calculations done at the QCISD(T)/6-311+G(3df,2p)//MP2=FULL/6-31G(d) level of theory
Originally a Troe expression was given, only k_inf is taken here
""",
)