The anatomy of a chemical reaction: Dissection by machine learning algorithms

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This document discusses using machine learning algorithms to analyze chemical reaction data. It describes how current reaction reporting formats are not well-suited for computational analysis. A more structured reporting format is proposed to fully describe reactions in a digitally friendly way, including specifying reactants, products, quantities, yields, and metrics like atom efficiency. This structured data would allow modeling of reaction substitutability and enable large-scale machine learning of chemical transformations.

Ciências

The anatomy of a
chemical reaction:
Dissection by machine
learning algorithms
Alex M. Clark, Ph.D.
August 2014
© 2015 Molecular Materials Informatics, Inc.
http://molmatinf.com

MOLECULAR MATERIALS INFORMATICS
21st Century Publishing
2
chemist
experiment
write up
conﬁrm
μ pub
URI
viewing
searching
machine
learning

MOLECULAR MATERIALS INFORMATICS
All your byte are belong to us
• Just because a reaction scheme is digital…
• … doesn’t mean it’s of any use to a computer.
3

MOLECULAR MATERIALS INFORMATICS
Production Raster Graphics
4
Generic molfile
15 16 0 0 0 0 0 0 0 0999 V2000
-3.9510 4.0500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.2500 3.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6519 3.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.2500 1.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.9510 1.0500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6519 1.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2306 3.7694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3482 2.5611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2240 1.3407 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-6.5490 4.0500 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
-7.8481 3.3000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-6.5490 5.5500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.1518 2.5673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9072 1.2714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8964 3.8695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 2 0 0 0 0
2 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 3 1 0 0 0 0
3 7 1 0 0 0 0
7 8 2 0 0 0 0
8 9 1 0 0 0 0
9 6 1 0 0 0 0
2 10 1 0 0 0 0
10 11 1 0 0 0 0
10 12 2 0 0 0 0
8 13 1 0 0 0 0
13 14 1 0 0 0 0
13 15 1 0 0 0 0
M CHG 2 10 1 11 -1
M END

MOLECULAR MATERIALS INFORMATICS
Production Vector Graphics
• Manuscripts usually delivered as PDFs:
5

MOLECULAR MATERIALS INFORMATICS
Spreadsheets
• Data gives the impression of organisation
• Very high degrees of freedom, nothing for structures
6

MOLECULAR MATERIALS INFORMATICS
Common Scheme
7

MOLECULAR MATERIALS INFORMATICS
Digitally Friendly
8
primary
reactant
secondary
reactants
catalyst
solvent
intermediate
byproducts
ﬁnal
product
reagent

MOLECULAR MATERIALS INFORMATICS
Representation
• For machines: representation
must be very rigidly deﬁned
• For humans: can generate
diagram programmatically
• MDL RXN/RDﬁle ~50% there
• DataSheet XML with Experiment
aspect
http://molmatinf.com/fmtaspect.html
9
StructureStep Role
1
1
1
1
1
1
2
2
Reactant
Reagent
Product
Product
Stoich.
1
1
1
1
1
1
1
1
Reactant
Reagent
Reagent
Reagent

MOLECULAR MATERIALS INFORMATICS
Balancing
10

MOLECULAR MATERIALS INFORMATICS
Quantities
11

MOLECULAR MATERIALS INFORMATICS
Green Metrics
12
• Totals for reactants, products & waste
• For each non-waste product: yield, PMI, E-factor,
Atom-E… always calculated, always recorded

MOLECULAR MATERIALS INFORMATICS 13
Reaction Transforms
• Reaction = speciﬁc description of experiment
1 2 3
4
1 2
3
4
• Transform = the generic form of a reaction

MOLECULAR MATERIALS INFORMATICS 14
Convenience
• Apply to a molecule...
10 g

MOLECULAR MATERIALS INFORMATICS 15
Decision MakingProductSearchResults
Yield PMI E-factor
Atom
Economy
100% 2.18 1.18 100%
84% 12.49 11.49 93.3%
82% 19.17 18.17 87.4%
100% 8.26 7.26 56.3%
63% 8.93 7.93 73.3%

MOLECULAR MATERIALS INFORMATICS
Model Building
• Most reaction data is noisy and incomplete
• Imagine opportunities with quantity & quality...
16
1
2
3
4
5 1
2
3
4
5
1
2
3
4
5
1
2
3
4
5
• For example: model solvent substitution

MOLECULAR MATERIALS INFORMATICS
Conclusions & Future
• Most published reactions intractible to machines
• Most reaction informatics formats 50% complete
• Full description has immediate beneﬁts...
• ... eventual large scale machine learning.
• μPublications with provenance: the path to open
repositories - but requires attention to content
17

Acknowledgments
http://molmatinf.com
http://molsync.com
http://cheminf20.org
@aclarkxyz
• Antony Williams
• Sean Ekins
• Leah McEwen
• Open data advocates
• Inquiries to
info@molmatinf.com

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2. MOLECULAR MATERIALS INFORMATICS 21st Century Publishing 2 chemist experiment write up conﬁrm μ pub URI viewing searching machine learning

3. MOLECULAR MATERIALS INFORMATICS All your byte are belong to us • Just because a reaction scheme is digital… • … doesn’t mean it’s of any use to a computer. 3

4. MOLECULAR MATERIALS INFORMATICS Production Raster Graphics 4 Generic molfile 15 16 0 0 0 0 0 0 0 0999 V2000 -3.9510 4.0500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2500 3.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6519 3.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2500 1.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9510 1.0500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6519 1.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2306 3.7694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3482 2.5611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2240 1.3407 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.5490 4.0500 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 -7.8481 3.3000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -6.5490 5.5500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1518 2.5673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9072 1.2714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8964 3.8695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 2 0 0 0 0 2 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 3 1 0 0 0 0 3 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 6 1 0 0 0 0 2 10 1 0 0 0 0 10 11 1 0 0 0 0 10 12 2 0 0 0 0 8 13 1 0 0 0 0 13 14 1 0 0 0 0 13 15 1 0 0 0 0 M CHG 2 10 1 11 -1 M END

5. MOLECULAR MATERIALS INFORMATICS Production Vector Graphics • Manuscripts usually delivered as PDFs: 5

6. MOLECULAR MATERIALS INFORMATICS Spreadsheets • Data gives the impression of organisation • Very high degrees of freedom, nothing for structures 6

7. MOLECULAR MATERIALS INFORMATICS Common Scheme 7

8. MOLECULAR MATERIALS INFORMATICS Digitally Friendly 8 primary reactant secondary reactants catalyst solvent intermediate byproducts ﬁnal product reagent

9. MOLECULAR MATERIALS INFORMATICS Representation • For machines: representation must be very rigidly deﬁned • For humans: can generate diagram programmatically • MDL RXN/RDﬁle ~50% there • DataSheet XML with Experiment aspect http://molmatinf.com/fmtaspect.html 9 StructureStep Role 1 1 1 1 1 1 2 2 Reactant Reagent Product Product Stoich. 1 1 1 1 1 1 1 1 Reactant Reagent Reagent Reagent

10. MOLECULAR MATERIALS INFORMATICS Balancing 10

11. MOLECULAR MATERIALS INFORMATICS Quantities 11

12. MOLECULAR MATERIALS INFORMATICS Green Metrics 12 • Totals for reactants, products & waste • For each non-waste product: yield, PMI, E-factor, Atom-E… always calculated, always recorded

13. MOLECULAR MATERIALS INFORMATICS 13 Reaction Transforms • Reaction = speciﬁc description of experiment 1 2 3 4 1 2 3 4 • Transform = the generic form of a reaction

14. MOLECULAR MATERIALS INFORMATICS 14 Convenience • Apply to a molecule... 10 g

15. MOLECULAR MATERIALS INFORMATICS 15 Decision MakingProductSearchResults Yield PMI E-factor Atom Economy 100% 2.18 1.18 100% 84% 12.49 11.49 93.3% 82% 19.17 18.17 87.4% 100% 8.26 7.26 56.3% 63% 8.93 7.93 73.3%

16. MOLECULAR MATERIALS INFORMATICS Model Building • Most reaction data is noisy and incomplete • Imagine opportunities with quantity & quality... 16 1 2 3 4 5 1 2 3 4 5 1 2 3 4 5 1 2 3 4 5 • For example: model solvent substitution

17. MOLECULAR MATERIALS INFORMATICS Conclusions & Future • Most published reactions intractible to machines • Most reaction informatics formats 50% complete • Full description has immediate beneﬁts... • ... eventual large scale machine learning. • μPublications with provenance: the path to open repositories - but requires attention to content 17

18. Acknowledgments http://molmatinf.com http://molsync.com http://cheminf20.org @aclarkxyz • Antony Williams • Sean Ekins • Leah McEwen • Open data advocates • Inquiries to info@molmatinf.com

The anatomy of a chemical reaction: Dissection by machine learning algorithms

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