12.3. Kinetics Database

This section describes the general usage of RMG’s kinetic database. See Modifying the Kinetics Database for instructions on modifying the database.

Pressure independent reaction rates in RMG are calculated using a modified Arrhenius equation, designating the reaction coefficient as \(k(T)\) at temperature \(T\).

\[k(T) = A\left(\frac{T}{T_0}\right)^ne^{-(E_0 + \alpha \Delta H_{rxn})/(RT)}\]

\(R\) is the universal gas constant. The kinetic parameters determining the rate coefficient are:

• \(A\): the pre-exponential A-factor

• \(T_0\): the reference temperature

• \(n\): the temperature exponent

• \(E_0\): the activation energy for a thermoneutral reaction (a barrier height intrinsic to the kinetics family)

• \(\alpha\): the Evans-Polanyi coefficient (characterizes the position of the transition state along the reaction coordinate, \(0 \le \alpha \le 1\))

• \(\Delta H_{rxn}\): the enthalpy of reaction

When Evans-Polanyi corrections are used, \(\Delta H_{rxn}\) is calculated using RMG’s thermo database, instead of being specified in the kinetic database. When Evans-Polanyi corrections are not used, \(\Delta H_{rxn}\) and \(\alpha\) are set to zero, and \(E_0\) is the activation energy of the reaction.

12.3.1. Libraries

Kinetic libraries delineate kinetic parameters for specific reactions. RMG always chooses to use kinetics from libraries over families. If multiple libraries contain the same reaction, then precedence is given to whichever library is listed first in the input.py file.

For combustion mechanisms, you should always use at least one small-molecule combustion library, such as the pre-packaged BurkeH2O2 and/or FFCM1 for natural gas. The reactions contained in these libraries are poorly estimated by kinetic families and are universally important to combustion systems.

Kinetic libraries should also be used in the cases where:

• A set of reaction rates were optimized together

• You know the reaction rate is not generalizable to similar species (perhaps due to catalysis or aromatic structures)

• No family exists for the class of reaction

• You are not confident about the accuracy of kinetic parameters

Below is a list of pre-packaged kinetics library reactions in RMG:

Library	Description
1989_Stewart_2CH3_to_C2H5_H	Chemically Activated Methyl Recombination to Ethyl (2CH3 -> C2H5 + H)
2001_Tokmakov_H_Toluene_to_CH3_Benzene	H + Toluene = CH3 + Benzene
2005_Senosiain_OH_C2H2	pathways on the OH + acetylene surface
2006_Joshi_OH_CO	pathways on OH + CO = HOCO = H + CO2 surface
2009_Sharma_C5H5_CH3_highP	Cyclopentadienyl + CH3 in high-P limit
2015_Buras_C2H3_C4H6_highP	Vinyl + 1,3-Butadiene and other C6H9 reactions in high-P limit
biCPD_H_shift	Sigmatropic 1,5-H shifts on biCPD PES
BurkeH2O2inArHe	Comprehensive H2/O2 kinetic model in Ar or He atmosphere
BurkeH2O2inN2	Comprehensive H2/O2 kinetic model in N2 atmosphere
C2H4+O_Klipp2017	C2H4 + O intersystem crossing reactions, probably important for all C/H/O combustion
C10H11	Cyclopentadiene pyrolysis in the presence of ethene
C3	Cyclopentadiene pyrolysis in the presence of ethene
C6H5_C4H4_Mebel	Formation Mechanism of Naphthalene and Indene
Chernov	Soot Formation with C1 and C2 Fuels (aromatic reactions only)
CurranPentane	Ignition of pentane isomers
Dooley	Methyl formate (contains several mechanisms)
ERC-FoundationFuelv0.9	Small molecule combustio (natural gas)
Ethylamine	Ethylamine pyrolysis and oxidation
FFCM1(-)	Foundational Fuel Chemistry Model Version 1.0 (excited species removed)
First_to_Second_Aromatic_Ring/2005_Ismail_C6H5_C4H6_highP	Phenyl + 1,3-Butadiene and other C10H11 reactions in high-P limit
First_to_Second_Aromatic_Ring/2012_Matsugi_C3H3_C7H7_highP	Propargyl + Benzyl and other C10H10 reactions in high-P limit
First_to_Second_Aromatic_Ring/2016_Mebel_C9H9_highP	C9H9 reactions in high-P limit
First_to_Second_Aromatic_Ring/2016_Mebel_C10H9_highP	C10H9 reactions in high-P limit
First_to_Second_Aromatic_Ring/2016_Mebel_Indene_CH3_highP	CH3 + Indene in high-P limit
First_to_Second_Aromatic_Ring/2017_Buras_C6H5_C3H6_highP	Phenyl + Propene and other C9H11 reactions in high-P limit
First_to_Second_Aromatic_Ring/2017_Mebel_C6H4C2H_C2H2_highP	C10H7 HACA reactions in high-P limit
First_to_Second_Aromatic_Ring/2017_Mebel_C6H5_C2H2_highP	C8H7 HACA reactions in high-P limit
First_to_Second_Aromatic_Ring/2017_Mebel_C6H5_C4H4_highP	Phenyl + Vinylacetylene and other C10H9 reactions in high-P limit
First_to_Second_Aromatic_Ring/2017_Mebel_C6H5C2H2_C2H2_highP	C10H9 HACA reactions in high-P limit
First_to_Second_Aromatic_Ring/phenyl_diacetylene_effective	Effective Phenyl + Diacetylene rates to Benzofulvenyl and 2-Napthyl
Fulvene_H	Cyclopentadiene pyrolysis in the presence of ethene
GRI-HCO	The HCO <=> H + CO reaction
GRI-Mech3.0	Gas Research Institute natural gas mechanism optimized for 1 atm (discontinued Feb. 2000)
GRI-Mech3.0-N	GRI-Mech3.0 including nitrogen chemistry (NOx from N2)
Glarborg	Mechanisms by P. Glarborg, assorted by carbon number
JetSurF2.0	Jet Surrogate Fuel model up tp C12 (excited species removed)
Klippenstein_Glarborg2016	Methane oxidation at high pressures and intermediate temperatures
Lai_Hexylbenzene	Alkylaromatic reactions for hexylbenzene
Mebel_C6H5_C2H2	Pathways from benzene to naphthalene
Mebel_Naphthyl	Reactions of naphthyl-1 and naphthyl-2
Methylformate	Methyl formate
Narayanaswamy	Oxidation of substituted aromatic species (aromatic reactions only)
Nitrogen_Dean_and_Bozzelli	Combustion Chemistry of Nitrogen
Nitrogen_Glarborg_Gimenez_et_al	High pressure C2H4 oxidation with nitrogen chemistry
Nitrogen_Glarborg_Lucassen_et_al	Fuel-nitrogen conversion in the combustion of small amines
Nitrogen_Glarborg_Zhang_et_al	Premixed nitroethane flames at low pressure
NOx	important NOx related reactions, e.g., thermal & prompt NO, N2O
NOx/LowT	Low temperature kinetics (~<1000K) for selected reactions from the NOx library
OxygenSingTrip	Reactions of singlet and triplet oxygen
SOx	important SOx related reactions, e.g., H-S, C-S, SOx
Sulfur/DMDS	Dimethyl disulfide (CH3SSCH3)
Sulfur/DMS	Dimethyl disulfide (CH3SSCH3)
Sulfur/DTBS	Di-tert-butyl Sulfide (C4H9SSC4H9)
Sulfur/GlarborgBozzelli	SO2 effect on moist CO oxidation with and without NO
Sulfur/GlarborgH2S	H2S oxidation at high pressures
Sulfur/GlarborgMarshall	OCS chemistry
Sulfur/GlarborgNS	Interactions between nitrogen and sulfur species in combustion
Sulfur/Hexanethial_nr	Hexyl sulfide (C6H13SC6H13) + hexadecane (C16H34)
Sulfur/Sendt	Small sulfur molecule
Sulfur/TP_Song	Thiophene (C4H4S, aromatic)
Sulfur/Thial_Hydrolysis	Thioformaldehyde (CH2S) and thioacetaldehyde (C2H4S) to COS and CO2
TEOS	Organic oxidized silicone
c-C5H5_CH3_Sharma	Cyclopentadienyl + CH3
combustion_core	Leeds University natural gas mechanism (contains versions 2-5)
fascella	Cyclopentadienyl + acetyl
kislovB	Formation of indene in combustion
naphthalene_H	Cyclopentadiene pyrolysis in the presence of ethene Part 1
vinylCPD_H	Cyclopentadiene pyrolysis in the presence of ethene Part 2
PrimaryH2O2	Updated rate parameters for the H2O2 system that include ter-molecular reactions

12.3.2. Families

Allowable reactions in RMG are divided up into classes called reaction families. All reactions not listed in a kinetic library have their kinetic parameters estimated from the reaction families.

Each reaction family contains the files:

• groups.py containing the recipe, group definitions, and hierarchical trees

• training.py containing a training set for the family

• rules.py containing kinetic parameters for rules

There are currently 74 reaction families in RMG:

1+2_Cycloaddition
1,2-Birad_to_alkene
1,2_Insertion_CO
1,2_Insertion_carbene
1,2_NH3_elimination
1,2_shiftC
1,2_shiftS
1,3_Insertion_CO2
1,3_Insertion_ROR
1,3_Insertion_RSR
1,3_NH3_elimination
1,3_sigmatropic_rearrangement
1,4_Cyclic_birad_scission
1,4_Linear_birad_scission
2+2_cycloaddition
6_membered_central_C-C_shift
Baeyer-Villiger_step1_cat
Baeyer-Villiger_step2
Baeyer-Villiger_step2_cat
Bimolec_Hydroperoxide_Decomposition
Birad_R_Recombination
Birad_recombination
CO_Disproportionation
Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH
Cyclic_Ether_Formation
Cyclic_Thioether_Formation
Cyclopentadiene_scission
Diels_alder_addition
Disproportionation
HO2_Elimination_from_PeroxyRadical
H_Abstraction
Intra_2+2_cycloaddition_Cd
Intra_5_membered_conjugated_C=C_C=C_addition
Intra_Diels_alder_monocyclic
Intra_Disproportionation
Intra_RH_Add_Endocyclic
Intra_RH_Add_Exocyclic
Intra_R_Add_Endocyclic
Intra_R_Add_ExoTetCyclic
Intra_R_Add_Exo_scission
Intra_R_Add_Exocyclic
Intra_Retro_Diels_alder_bicyclic
Intra_ene_reaction
Korcek_step1
Korcek_step1_cat
Korcek_step2
Peroxyl_Disproportionation
Peroxyl_Termination
R_Addition_COm
R_Addition_CSm
R_Addition_MultipleBond
R_Recombination
Singlet_Carbene_Intra_Disproportionation
Singlet_Val6_to_triplet
SubstitutionS
Substitution_O
Surface_Abstraction
Surface_Adsorption_Bidentate
Surface_Adsorption_Dissociative
Surface_Adsorption_Double
Surface_Adsorption_Single
Surface_Adsorption_vdW
Surface_Bidentate_Dissociation
Surface_Dissociation
Surface_Dissociation_vdW
Surface_Recombination
intra_H_migration
intra_NO2_ONO_conversion
intra_OH_migration
intra_substitutionCS_cyclization
intra_substitutionCS_isomerization
intra_substitutionS_cyclization
intra_substitutionS_isomerization
lone_electron_pair_bond

12.3.2.1. Recipe

The recipe can be found near the top of groups.py and describes the changes in bond order and radicals that occur during the reaction. Reacting atoms are labelled with a starred number. Shown below is the recipe for the H-abstraction family.

The table below shows the possible actions for recipes. The arguments are given in the curly braces as shown above. For the order of bond change in the Change_Bond action, a -1 could represent a triple bond changing to a double bond while a +1 could represent a single bond changing to a double bond.

Action	Argument1	Argument2	Argument3
Break_Bond	First bonded atom	Type of bond	Second bonded atom
Form_Bond	First bonded atom	Type of bond	Second bonded atom
Change_Bond	First bonded atom	Order of bond change	Second bonded atom
Gain_Radical	Specified atom	Number of radicals
Lose_Radical	Specified atom	Number of radicals

Change_Bond order cannot be directly used on benzene bonds. During generation, aromatic species are kekulized to alternating double and single bonds such that reaction families can be applied. However, RMG cannot properly handle benzene bonds written in the kinetic group definitions.

12.3.2.2. Training Set vs Rules

The training set and rules both contain trusted kinetics that are used to fill in templates in a family. The training set contains kinetics for specific reactions, which are then matched to a template. The kinetic rules contain kinetic parameters that do not necessarily correspond to a specific reaction, but have been generalized for a template.

When determining the kinetics for a reaction, a match for the template is searched for in the kinetic database. The three cases in order of decreasing reliability are:

1. Reaction match from training set

2. Node template exact match using either training set or rules

3. Node template estimate averaged from children nodes

Both training sets and reaction libraries use the observed rate, but rules must first be divided by the degeneracy of the reaction. For example, the reaction CH4 + OH –> H2O + CH3 has a reaction degeneracy of 4. If one performed an experiment or obtained this reaction rate using Arkane (applying the correct symmetry), the resultant rate parameters would be entered into libraries and training sets unmodified. However a kinetic rule created for this reaction must have its A-factor divided by 4 before being entered into the database.

The reaction match from training set is accurate within the documented uncertainty for that reaction. A template exact match is usually accurate within about one order of magnitude. When there is no kinetics available for for the template in either the training set or rules, the kinetics are averaged from the children nodes as an estimate. In these cases, the kinetic parameters are much less reliable. For more information on the estimation algorithm see Kinetics Estimation.

The training set can be modified in training.py and the rules can be modified in rules.py. For more information on modification see Adding Training Reactions and Adding Kinetic Rules.