12.1. Introduction

This section describes some of the general characteristics of RMG’s databases.

12.1.1. Group Definitions

The main section in many of RMG’s databases are the ‘group’ definitions. Groups are adjacency lists that describe structures around the reacting atoms. Between the adjacency list’s index number and atom type, a starred number is inserted if the atom is a reacting atom.

Because groups typically do not describe entire molecules, atoms may appear to be lacking full valency. When this occurs, the omitted bonds are allowed to be anything. An example of a primary carbon group from H-Abstraction is shown below. The adjacency list defined on the left matches any of the three drawn structures on the right (the numbers correspond to the index from the adjacency list).

Atom types describe atoms in group definitions. The table below shows all atoms types in RMG.

Atom Type	Chemical Element	Localized electronic structure
R	Any	No requirements
R!H	Any except hydrogen	No requirements
H	Hydrogen	No requirements
C	Carbon	No requirements
Ca	Carbon	Atomic carbon with two lone pairs and no bonds
Cs	Carbon	Up to four single bonds
Csc	Carbon	Up to three single bonds, charged +1
Cd	Carbon	One double bond (to any atom other than O or S), up to two single bonds
Cdc	Carbon	One double bond, up to one single bond, charged +1
CO	Carbon	One double bond to an oxygen atom, up to two single bonds
CS	Carbon	One double bond to an sulfur atom, up to two single bonds
Cdd	Carbon	Two double bonds
Ct	Carbon	One triple bond, up to one single bond
Cb	Carbon	Two benzene bonds, up tp one single bond
Cbf	Carbon	Three benzene bonds (fused aromatics)
C2s	Carbon	One lone pair, up to two single bonds
C2sc	Carbon	One lone pair, up to three single bonds, charged -1
C2d	Carbon	One lone pair, one double bond
C2dc	Carbon	One lone pair, one double bond, up to one single bond, charge -1
C2tc	Carbon	One lone pair, one triple bond, charged -1
N	Nitrogen	No requirements
N0sc	Nitrogen	Three lone pairs, up to one single bond, charged -2
N1s	Nitrogen	Two lone pairs, up to one single bond
N1sc	Nitrogen	Two lone pairs, up to two single bonds, charged -1
N1dc	Nitrogen	Two lone pairs, one double bond, charged -1
N3s	Nitrogen	One lone pair, up to three single bonds
N3d	Nitrogen	One lone pair, one double bond, up to one single bond
N3t	Nitrogen	One lone pair, one triple bond
N3b	Nitrogen	One lone pair, two aromatic bonds
N5sc	Nitrogen	No lone pairs, up to four single bonds, charged +1
N5dc	Nitrogen	No lone pairs, one double bond, up to two single bonds, charged +1
N5ddc	Nitrogen	No lone pairs, two double bonds, charged +1
N5dddc	Nitrogen	No lone pairs, three double bonds, charged -1
N5tc	Nitrogen	No lone pairs, one triple bond, up to one single bond, charged +1
N5b	Nitrogen	No lone pairs, two aromatic bonds, up to one single bond
O	Oxygen	No requirements
Oa	Oxygen	Atomic oxygen with three lone pairs and no bonds
O0sc	Oxygen	Three lone pairs, up to one single bond, charged -1
O0dc	Oxygen	Three lone pairs, one double bond, charged -2
O2s	Oxygen	Two lone pairs, up to two single bonds
O2sc	Oxygen	Two lone pairs, up to one single bond, charged +1
O2d	Oxygen	Two lone pairs, one double bond
O4sc	Oxygen	One lone pair, up to three single bonds, charged +1
O4dc	Oxygen	One lone pair, one double bond, up to one single bond, charged +1
O4tc	Oxygen	One lone pair, one triple bond, charged +1
Si	Silicon	No requirements
Sis	Silicon	Up to four single bonds
Sid	Silicon	One double bond (not to O), up to two single bonds
SiO	Silicon	One double bond to an oxygen atom, up to two single bonds
Sidd	Silicon	Two double bonds
Sit	Silicon	One triple bond, up to one single bond
Sib	Silicon	Two benzene bonds, up tp one single bond
Sibf	Silicon	Three benzene bonds (fused aromatics)
P	Phosphorus	No requirements
P0sc	Phosphorus	Three lone pairs, up to one single bond, charged -2
P1s	Phosphorus	Two lone pairs, up to one single bond
P1sc	Phosphorus	Two lone pairs, up to two single bonds, charged -1
P1dc	Phosphorus	Two lone pairs, one double bond, charged -1
P3s	Phosphorus	One lone pair, up to three single bonds
P3d	Phosphorus	One lone pair, one double bond, up to one single bond
P3t	Phosphorus	One lone pair, one triple bond
P3b	Phosphorus	One lone pair, two aromatic bonds
P5s	Phosphorus	No lone pairs, up to five single bonds
P5sc	Phosphorus	No lone pairs, up to six single bonds, charged -1/+1/+2
P5d	Phosphorus	No lone pairs, one double bond, up to three single bonds
P5dd	Phosphorus	No lone pairs, two double bonds, up to one single bond
P5dc	Phosphorus	No lone pairs, one double bond, up to two single bonds, charged +1
P5ddc	Phosphorus	No lone pairs, two double bonds, charged +1
P5t	Phosphorus	No lone pairs, one triple bond, up to two single bonds
P5td	Phosphorus	No lone pairs, one triple bond, one double bond
P5tc	Phosphorus	No lone pairs, one triple bond, up to one single bond, charged +1
P5b	Phosphorus	No lone pairs, two aromatic bonds, up to one single bond, charged 0/+1
P5bd	Phosphorus	No lone pairs, two aromatic bonds, one double bond
S	Sulfur	No requirements
Sa	Sulfur	Atomic sulfur with three lone pairs and no bonds
S0sc	Sulfur	Three lone pairs, up to once single bond, charged -1
S2s	Sulfur	Two lone pairs, up to two single bonds
S2sc	Sulfur	Two lone pairs, up to three single bonds, charged -1/+1
S2d	Sulfur	Two lone pairs, one double bond
S2dc	Sulfur	Two lone pairs, one to two double bonds, up to one single bond, charged -1
S2tc	Sulfur	Two lone pairs, one triple bond, charged -1
S4s	Sulfur	One lone pair, up to four single bonds
S4sc	Sulfur	One lone pair, up to five single bonds, charged -1/+1
S4d	Sulfur	One lone pair, one double bond, up to two single bonds
S4dd	Sulfur	One lone pair, two double bonds
S4dc	Sulfur	One lone pair, one to three double bonds, up to three single bonds, charged -1/+1
S4b	Sulfur	One lone pair, two aromatic bonds
S4t	Sulfur	One lone pair, one triple bond, up to one single bond
S4tdc	Sulfur	One lone pair, one to two triple bonds, up to two double bonds, up to two single bonds, charged -1/+1
S6s	Sulfur	No lone pairs, up to six single bonds
S6sc	Sulfur	No lone pairs, up to seven single bonds, charged -1/+1/+2
S6d	Sulfur	No lone pairs, one double bond, up to four single bonds
S6dd	Sulfur	No lone pairs, two double bonds, up to two single bonds
S6ddd	Sulfur	No lone pairs, up to three double bonds
S6dc	Sulfur	No lone pairs, one to three double bonds, up to five single bonds, charged -1/-1/+2
S6t	Sulfur	No lone pairs, one triple bond, up to three single bonds
S6td	Sulfur	No lone pairs, one triple bond, one double bond, up to one single bond
S6tt	Sulfur	No lone pairs, two triple bonds
S6tdc	Sulfur	No lone pairs, one to two triple bonds, up to two double bonds, up to four single bonds, charged -1/-1
Cl	Chlorine	No requirements
Cl1s	Chlorine	Three lone pairs, zero to one single bonds
Br	Bromine	No requirements
Br1s	Bromine	Three lone pairs, zero to one single bonds
I	Iodine	No requirements
I1s	Iodine	Three lone pairs, zero to one single bonds
F	Fluorine	No requirements
F1s	Fluorine	Three lone pairs, zero to one single bonds
He	Helium	No requirements, nonreactive
Ne	Neon	No requirements, nonreactive
Ar	Argon	No requirements, nonreactive

Additionally, groups can also be defined as unions of other groups. For example,:

label="X_H_or_Xrad_H",
group=OR{X_H, Xrad_H},

12.1.2. Forbidden Groups

Forbidden groups can be defined to ban structures globally in RMG or to ban pathways in a specific kinetic family.

Globally forbidden structures will ban all reactions containing either reactants or products that are forbidden. These groups are stored in in the file located at RMG-database/input/forbiddenStructures.py.

To ban certain specific pathways in the kinetics families, a forbidden group must be created, like the following group in the intra_H_migration family:

forbidden(
    label = "bridged56_1254",
    group =
"""
1 *1 C 1 {2,S} {6,S}
2 *4 C 0 {1,S} {3,S} {7,S}
3    C 0 {2,S} {4,S}
4 *2 C 0 {3,S} {5,S} {8,S}
5 *5 C 0 {4,S} {6,S} {7,S}
6    C 0 {1,S} {5,S}
7    C 0 {2,S} {5,S}
8 *3 H 0 {4,S}
""",
    shortDesc = u"""""",
    longDesc =
u"""

""",
)

Forbidden groups should be placed inside the groups.py file located inside the specific kinetics family’s folder RMG-database/input/kinetics/family_name/ alongside normal group entries. The starred atoms in the forbidden group ban the specified reaction recipe from occurring in matched products and reactants.

In addition for forbidding groups, there is the option of forbidding specific molecules or species in RMG-database/input/forbiddenStructures.py. Forbidding a molecule will prevent that exact structure from being generated, while forbidding a species will prevent any of its resonance structures from being generated. Note that specific molecules or species can only be forbidden globally and should not be specified in the groups.py file. To specify a forbidden molecule or species, simply replace the group keyword with molecule or species:

# This forbids a molecule
forbidden(
    label = "C_quintet",
    molecule =
"""
multiplicity 5
1 C u4 p0
""",
    shortDesc = u"""""",
    longDesc =
u"""

""",
)

# This forbids a species
forbidden(
    label = "C_quintet",
    species =
"""
multiplicity 5
1 C u4 p0
""",
    shortDesc = u"""""",
    longDesc =
u"""

""",
)

12.1.3. Hierarchical Trees

Groups are ordered into the nodes of a hierarchical trees which is written at the end of groups.py. The root node of each tree is the most general group with the reacting atoms required for the family. Descending from the root node are more specific groups. Each child node is a subset of the parent node above it.

A simplified example of the trees for H-abstraction is shown below. The indented text shows the syntax in groups.py and a schematic is given underneath.

Individual groups only describe part of the reaction. To describe an entire reaction we need one group from each tree, which we call node templates or simply templates. (C_pri, O_pri_rad), (H2, O_sec_rad), and (X_H, Y_rad) are all valid examples of templates. Templates can be filled in with kinetic parameters from the training set or rules.