4-1. 1_MonomerDefiner.ipynb

The notebook 1_MonomerDefiner.ipynb is a utility script for defining and categorizing monomers based on their functional groups (FGs). It creates dictionaries and lists that define monomer types, their objective functional groups, and incompatible functional groups. These definitions are exported as JSON files for use in other parts of the project.

Key Components

1. Metadata
The notebook includes metadata about its purpose and references:

• Purpose: Define monomers and their functional groups.

• References: Links to SMARTS theory and examples for understanding chemical patterns.

2. Functional Group (FG) Definitions
The notebook defines objective and incompatible functional groups for each monomer type. These definitions are stored in two dictionaries:

• monL: Contains SMARTS patterns for objective functional groups.

• exclL: Contains SMARTS patterns for incompatible functional groups.

3. Monomer Dictionaries
The notebook defines dictionaries to map monomer names to numerical identifiers:

• mon_dic: Python dictionary of the monomer classes. Categorizes the values of “mon_dic.json” into self-polymerizable monomer systems, binary-monomer systems, post-polymerization reactions, and olefinic monomer systems.

  • key : monomer class

  • value : Allocated int.

    • 1 - 50 : for self-polymerizable system; eg. addition, ring-opening polymerization and self-condensation.

    • 51- 100 : for the polymerization system that require bi-monomer classes; eg. poly condensation, polyadditin and addition-condensation.

    • 1000 - : detailed classification for olefinic monomers.

• mon_dic_inv: Inverse mapping of mon_dic (from integers to names).

• mon_vals: A tuple categorized mon_dic values according to the corresponding polymerization reactions (see Table 5-1, 2, 3).

4. Monomer Definitions
Each monomer type is defined with:

• mon_lst.json (monL)
  List of the definition of the polymerization site for each monomer class. Contains SMARTS patterns for objective functional groups.

  • 1 - 50 : for self-polymerizable system; eg. addition, ring-opening polymerization and self-condensation.

  • 51- 100 : for the polymerization system that require bi-monomer classes; eg. poly condensation, polyadditin and addition-condensation.

  • 200 - post-polymerization reactions of residual polymerizable functional grous(s).

  • 1000 - for olefinic monomer systems.

• excl_lst.json (exclL)
  List of the definition of functional groups that should not coexist in a monomer molecule for each monomer class. Contains SMARTS patterns for incompatible functional groups.

5. Exporting Definitions
The monomer definitions are exported as JSON files for use in other scripts.

Correspondence Table of Numbers and Content

In following tables,

• Allocated numbers are corresponding to

  • values of mon_dic except 200-999

  • key of mon_dic_inv except 200-999

  • key of mon_lst and excl_lst

• Monomer classes are corresponding to corresponding to key of mon_dic and values of mon_dic_inv.

Table 4-1. Allocated numbers and defined monomer classes for self-polymerizable system

No.	monomer class	compounds
1	vinyl	vinylidene
2	epo	epoxide
3	cOle	cyclic olefin
4	lactone	lactone
5	lactam	lactam
6	hydCOOH	hydroxy carboxylic acid
7	aminCOOH	amino acid
8	hindPhenol	hindered phenol
9	cAnhyd	cyclic carboxylic acid anhydride
10	CO	carbon monoxide. Forced addition to synthesize carbonates
11	HCHO	form aldehyde. Forced addition for addition-condensation (future works)
12	sfonediX	bis(p-halo aryl)sulfone
13	BzodiF	bis(p-fluoro aryl)ketone

Table 4-2. Allocated numbers and defined monomer classes for the polymerization system that require bi-monomer classes

No.	monomer class	compounds
51	diepo	di/polyepoxide
52	diCOOH	di/polycarboxylic acid and acid halide
53	diol	primary and secodary di/polyol, di/polythiol and /polyphenol
54	diamin	di/polyamine
55	diNCO	di/polyisocyanate
56	dicAnhyd	bis/poly(cyclic carboxylic acid anhydride)
57	pridiamin	di/polyprimary diamine
58	diol_b	primary and secodary di/polyol, di/polyphenol

Table 4-3. Allocated numbers and defined monomer classes for olefinic monomers

No.	monomer class	compounds
1001	acryl	acrylate
1002	bEWole	beta-ectron withdrawing group substituted olefin
1003	styryl	styryl
1004	allyl	allyl
1005	haloCH	halogenated olefin
1006	vinylester	vinyl ester
1007	malei	maleic imide derivatives
1020	conjdiene	conjugated dienes
1030	vinylether	vinyl ether
1031	tertcatCH	beta-disubstituded aliphatic olefin
1050	cycCH	alycyclic olefin
1052	aliphCH	aliphatic olefin

Table 4-4. post-polymerization reactions of residual polymerizable functional grous(s)

No.	SMARTS	Residual functional group
200	[CX3]=[CX3]	olefin
201	[CX4;R]1[OX2;R][CX4;R]1	epoxide
202	[CX3](=[O])[OX2H1,F,Cl,Br,I]	carboxylic acid and acyl halide
203	[C,c][OX2,SX2;H1;!$([O,S]C=*)]	hydroxyl in alcohol and phenol
204	[C,c][NX3;H2;!$(N[C,S]=*)]	amine
205	[NX2]=[CX2]=[OX1,SX1]	isocyanate
206	[C,c][CX3,c;R](=[OX1])[OX2,o;R][CX3,c;R](=[OX1])[C,c]	carboxylic acid anhydride