Introduction to bigSMILES with examples

1. BigSMILES Workbook
Monet Phase II Kick-off Meeting
September 16-17, 2021
Brad Olsen and Haley Beech

2. Welcome to the world of BigSMILES
The best resource for an overview of the language:
https://olsenlabmit.github.io/BigSMILES/docs/line_notation.html#the-bigsmiles-line-notation
General steps for writing in BigSMILES:
1. Write the atoms in the monomers:
CC(c1ccccc1)
2. Add the bonding descriptors:
[$]CC(c1ccccc1)[$]
3. Assemble the stochastic object(s):
{[$]CC(c1ccccc1)[$]}
4. Specify end groups:
{[][$]CC(c1ccccc1)[$][]}
Strings do not require end
groups! Terminal bonding
descriptors should still be
included even if they are empty.

3. Example 1: Polyisoprene
1. Write the atoms in the monomers:
C/C=C/(C)C
2. Add the bonding descriptors:
[$]C/C=C/(C)C[$]
3. Assemble the stochastic object(s):
{[$]C/C=C/(C)C[$]}
4. Specify end groups:
{[][$]C/C=C/(C)C[$][]}
But what about the other isomers?
Since BigSMILES is stochastic, all potential structures should
be included, even if they form only in small amounts.
{[][$]C/C=C(C)C[$][]} {[][$]CC(C(C)=C[$][]} {[][$]CC(C)(C=C)[$][]}
To denote a mixture use a comma delimited list:
{[][$]C/C=C/(C)C[$],
[$]C/C=C(C)C[$],
[$]CC(C(C)=C[$],
[$]CC(C)(C=C)[$][]}

4. Example 2: Nylon 6,6
1. Write the atoms in the monomers:
C(=O)CCCCC(=O),NCCCCCCN
2. Add the bonding descriptors:
[<]C(=O)CCCCC(=O)[<],[>]NCCCCCCN[>]
3. Assemble the stochastic object(s):
{[<]C(=O)CCCCC(=O)[<],[>]NCCCCCCN[>]}
4. Specify end groups:
{[][<]C(=O)CCCCC(=O)[<],[>]NCCCCCCN[>][]}
There are multiple representations for this
polymer, depending on if it is denoted as
two monomers or one. Both are valid!
The alternative representation is:
{[][<]C(=O)CCCCC(=O)NCCCCCCN[>][]}

5. Example 3: Vinyl-terminated PDMS
1. Write the atoms in the monomers:
[Si](C)(C)O
2. Add the bonding descriptors:
[>][Si](C)(C)O[<]
3. Assemble the stochastic object(s):
{[>][Si](C)(C)O[<]}
4. Specify end groups:
C=C{[<][>][Si](C)(C)O[<][>]}[Si](C)(C)C=C
End groups go outside of the
stochastic curly brackets but the
bonding descriptors go inside.

6. Example 4: Using the BigSMILES converter tool
Hosted on the CRIPT website:
http://criptapp.herokuapp.com/bigsmiles_converter
Try to practice with a couple previous
examples like nylon and polystyrene.
Steps:
1. Draw the chemical structure
2. Select repeat unit atoms
3. Click the bracket button [ ]
4. Select SRU polymer and hit ok
5. Hit the BigSMILES button {:)}
6. BigSMILES generated!
You can also copy and paste a structure in from ChemDraw
1. Copy as MOL text in ChemDraw
2. Re-select polymer and add SRU brackets
Watch the video on the website for a basic summary and overview.

7. Pair activity
1. Draw your favorite polymer and write down the corresponding BigSMILES string
(either on paper or with the converter)
2. We’ll put you in a breakout room with a partner. Introduce yourself!
3. Send the BigSMILES string to your partner in the chat
4. Have them share their screen and draw it on the whiteboard. See if it matches
what you had drawn originally.
Ready? Set? Smile!

8. Example 5: Block copolymer
1. Write the atoms in the monomers:
CCO,CC(C)O
2. Add the bonding descriptors:
[<]CCO[>],[<]CC(C)O[>]
3. Assemble the stochastic object(s):
{[<]CCO[>]},{[<]CC(C)O[>]}
4. Specify end groups:
{[][<]CCO[>][<]},{[>][<]CC(C)O[>][]}
PEO-b-PPO
In this case, the "end group" for
each polymeric segment is
another polymer segment.

9. Example 6: Randomly crosslinked polyacrylamide gel
1. Write the atoms in the monomers:
CC(C(=O)N),CC(C(=O)NCNC(=O))CC
2. Add the bonding descriptors:
[$]CC(C(=O)N)[$],
[$]CC(C(=O)NCNC(=O)C[$]C[$])[$]
3. Assemble the stochastic object(s):
{[$]CC(C(=O)N)[$],
[$]CC(C(=O)NCNC(=O)C[$]C[$])[$]}
4. Specify end groups:
{[][$]CC(C(=O)N)[$],
[$]CC(C(=O)NCNC(=O)C[$]C[$])[$][]}
+

10. Example 7: Tetra-PEG network
1. Write the atoms in the monomers:
#Arm1=COCCOCCCN.
#Arm2=COCCOCOCCCC(=O)
2. Add the bonding descriptors:
#Arm1=CO[>]CCO[<]CCCN.
#Arm2=CO[>]CCO[<]COCCCC(=O)
3. Assemble the stochastic object(s):
{#Arm1=CO{[>][<]CCO[>][<]}CCCN}.{#Arm2=CO{[>][<]CCO[>][<]}COCCCC(=O)}.
{C([#Arm1][<])([#Arm1][<])([#Arm1][<]) [#Arm1][<],
C([#Arm2][>])([#Arm2][>])([#Arm2][>])[#Arm2][>]}
4. Specify end groups:
{#Arm1=CO{[>][<]CCO[>][<]}CCCN}.{#Arm2=CO{[>][<]CCO[>][<]}COCCCC(=O)}.
{C([#Arm1][<])([#Arm1][<])([#Arm1][<]) [#Arm1][<],
C([#Arm2][>])([#Arm2][>])([#Arm2][>])[#Arm2][>];
[>][H],[<]ON1C(=O)CCC1(=O)}
For more complex
strings, stochastic
objects can be pre-
defined and nested
to simplify and
shorten notation.
Sakai et al., Macromolecules, 41(14), 2008.

11. Example 8: Random copolymer (charged)
Poly(oligoethyleneglycol-methacrylate-b-quaternized 4-vinylpyridine))
(POEGMA-b-qP4vP diblock)
1. Write the atoms in the monomers:
CC(C(=O)OCCOC),CC(c1ccncc1),CC(c1cc[n+]cc1).[I-]
2. Add the bonding descriptors:
[$]CC(C(=O)O[>]CCO[<]C)[$],[$]CC(c1ccncc1)[$],
[$]CC(c1ccncc1)[$].[I-]
3. Assemble the stochastic object(s):
{[$]CC(C(=O)O{[<][>]CCO[<][>]}C)[$],[$]CC(c1ccncc1)[$],
[$]CC(c1ccncc1)[$].[I-]}
4. Specify end groups:
OC(=O)CCC(C)(C#N){[$][$]CC(C(=O)O{[<][>]CCO[<][>]}C)[$],[$]CC(c1ccncc1)[$],
[$]CC(c1ccncc1)[$].[I-][$]}SC(=S)c1ccccc1

12. Advanced example: Vulcanized poly(1,3-butadiene)
1. Write the atoms in the monomers:
CC=CC,CCCC,S
2. Add the bonding descriptors:
CC=CC,CCCC,S
3. Assemble the stochastic object(s):
[$]CC=CC[$],[$]CC([<])C([>])C[$],[>]{[$][$]S[$][$]}[>]
4. Specify end groups:
{[][$]CC=CC[$],[$]CC([<])C([>])C[$],[>]{[$][$]S[$][$]}[>]}