4-2. 2_Ps_rxnL.ipynb

The notebook 2_Ps_rxnL.ipynb is a utility script for defining a list of polymerization reactions using RDKit’s SMARTS-based reaction definitions. It creates a dictionary Ps_rxnL that maps monomer types or reaction types to their corresponding chemical reactions. These reactions are later serialized into a pickle file (ps_rxn.pkl) for use in other parts of the project.

Key Components

Metadata
The notebook includes metadata about its purpose and references:

• Purpose: Define a list of polymerization reactions.

• References: Links to RDKit documentation and SMARTS theory for understanding reaction definitions.

Imports
The following libraries are imported:

• json: For loading monomer dictionary (mon_dic.json).

• pickle: For saving the reaction dictionary (Ps_rxnL) to a file.

• rdkit.Chem.AllChem: For creating chemical reactions from SMARTS strings.

Loading Monomer Dictionary
The monomer dictionary (mon_dic.json) is loaded to map monomer types (e.g., vinyl, epo) to numerical identifiers:

Reaction Definitions
The notebook defines a series of polymerization reactions using RDKit’s AllChem.ReactionFromSmarts function. These reactions are stored in the Ps_rxnL dictionary, where the keys are either numerical identifiers or descriptive names, and the values are RDKit reaction objects.　　 Note that polymerization reactions SMARS using detailed olefinic monomer classification except ROMP(H) and COC were automatically generated from corrsponding monomer by the function “smipoly.smip.funclib.ole_rxnsmarts_gen”.

Reaction Categories

1. Self-polymerizable Monomer Systems:

• Self-polymerization reactions to form homopolymers for monomers like vinyl, epoxide, cyclic olefins, lactones, lactams, etc.

2. Binary Monomer Systems:

• Olefin copolymerization reactions to form altanating copolymers by combinations of monomers (e.g., vinyl-vinyl, vinyl-cyclic olefin).

• Polymerization reaction which require essentialy bi-monomer classes (e.g. dicarboxylic acid + diol)

3. Sequential Reactions:

• Post-polymerization reactions for residual specific functional groups (e.g., epoxide, hydroxyl, carboxyl, amine).

4. Olefinic Monomers:

• Polymerization reactions using detailed olefinic monomer classification

• Reactions for cyclic olefins (e.g., ROMP, COC).

Saving the Reaction Dictionary
The Ps_rxnL dictionary is serialized and saved to a pickle file (ps_rxn.pkl) for later use.

Correspondence Table of Numbers and Content

The alocated number of polymerization reaction are key of Ps_rxnL.
The numbers within the square brackets in the monomer class correspond to the values of mon_dic and key of mon_dic_inv.

Table 4-5. Assigned polymerization reactions and corresponding monomer classes.

No. of Polymerization Reaction	Monomer Class 1	Monomer Class 2	Reaction Type	Product
1	Vinyl [1]		Addition Chain Polymerization	Homopolymer
3	Cyclic Olefin [3]		Addition Chain Polymerization	Homopolymer
101	Vinyl [1]	Vinyl [1]	Addition Chain Polymerization	Alternating copolymer
102	Vinyl [1]	Cyclic Olefin [3]	Addition Chain Polymerization	Alternating copolymer
103	Cyclic Olefin [3]	Cyclic Olefin [3]	Addition Chain Polymerization	Alternating copolymer
4	Lactone [4]		Ring-Opening Chain Polymerization	Homopolymer
6	Hydroxy Carboxylic Acid [6]		Polycondensation	Homopolymer
105	Hydroxy Carboxylic Acid [6]	Hydroxy Carboxylic Acid [6]	Polycondensation	Alternating copolymer
104	Di/Polycarboxylic Acid [52]	Di/Polyol [53]	Polycondensation	Homopolymer
106	Di/Polyol [53]	Carbon Monoxide [10]	Polycondensation	Homopolymer
112	Cyclic Anhydride [9]	Epoxide [2]	Ring-Opening Chain Polymerization	Homopolymer
2	Epoxide [2]		Ring-Opening Chain Polymerization	Homopolymer
8	Hindered Phenol [8]		Polycondensation	Homopolymer
114	Bis(p-Halogenated Aryl)Sulfone [12]	Di/Polyol (Without Thiol) [58]	Polycondensation	Homopolymer
115	Bis(p-Fluoroaryl)Ketone [13]	Di/Polyol (Without Thiol) [58]	Polycondensation	Homopolymer
5	Lactam [5]		Ring-Opening Chain Polymerization	Homopolymer
7	Amino Acid [7]		Polycondensation	Homopolymer
109	Amino Acid [7]	Amino Acid [7]	Polycondensation	Alternating copolymer
108	Di/Polycarboxylic Acid [52]	Di/Polyamine [54]	Polycondensation	Homopolymer
110	Di/Polycyclic Anhydride [56]	Primary Di/Polyamine [57]	Polycondensation	Homopolymer
111	Di/Polyisocyanate [55]	Di/Polyol [53]	Polyaddition	Homopolymer
113	Di/Polyepoxide [51]	Di/Polyisocyanate [55]	Polyaddition	Homopolymer

Table 4-6. Post-polymerization reactions of residual polymerizable functional grous(s) for the Function “bipolym”.

No. of Applied Polymerization Reaction	Reaction Class	Residual Functional Group
1, 3, 101, 102, 103	200	olefin
112	201	epoxide
4, 5, 6, 7, 104, 105, 108, 109	202	carboxylic acid and acyl halide
4, 5, 6, 104, 105, 111, 114, 115	203	hydroxyl in alcohol and phenol
4, 5, 7	204	amine
111	205	isocyanate
112	206	carboxylic acid anhydride
110	207	carboxylic acid anhydride
113	208	isocyanate

Table 4-7. Assigned polymerization reactions for detail classified olefinic monomer.

Applied Polymerization Reaction of Olefinic Monomer	Reaction Class	Monomer Class / Residual Functional Group
ROMP	1050	cycCH [1050]
COC	1051	cycCH [1050] in COC
COC	1051	aliphCH [1052] in COC
Detail Classified Polyolefin Containing Diene Monomer	209	isomerize 1,2-added diene to 1,4-addition
ROMPH	210	olefin hydrogenation on ROMPH