Building a mobile
reaction lab notebook
Alex M. Clark, Ph.D.
March 2014
© 2014 Molecular Materials Informatics, Inc.!
http...
MOLECULAR MATERIALS INFORMATICS
Electronic Lab Notebooks
• Many shapes & sizes: big, small, hosted,
desktop, mobile
• Doma...
MOLECULAR MATERIALS INFORMATICS
Data Capture
• Reactions normally drawn for chemists…
!3
• … rather than computers.
MOLECULAR MATERIALS INFORMATICS
Data Capture
• Reactions normally drawn for chemists…
!3
• … rather than computers.
MOLECULAR MATERIALS INFORMATICS
Digitally Friendly
!4
MOLECULAR MATERIALS INFORMATICS
Digitally Friendly
!4
primary!
reactant
secondary!
reactants
catalyst
solvent
intermediate...
MOLECULAR MATERIALS INFORMATICS
Functionality
• Priorities:
1. computer-friendly datastructures
2. human-friendly workflow
...
MOLECULAR MATERIALS INFORMATICS
Yield101
• Prior art: designed
originally for
education
• Fancy reaction
quantity calculat...
MOLECULAR MATERIALS INFORMATICS
Green Lab Notebook
• Under construction as an iOS
app (phones & tablets)
• Superset of Yie...
MOLECULAR MATERIALS INFORMATICS
A New Experiment
• Start with a fresh slate: select
the reactant placeholder
• Select the ...
MOLECULAR MATERIALS INFORMATICS
A New Experiment
• Start with a fresh slate: select
the reactant placeholder
• Select the ...
MOLECULAR MATERIALS INFORMATICS
A New Experiment
• Start with a fresh slate: select
the reactant placeholder
• Select the ...
MOLECULAR MATERIALS INFORMATICS
A New Experiment
• Start with a fresh slate: select
the reactant placeholder
• Select the ...
MOLECULAR MATERIALS INFORMATICS
The First Step
• Draw product
• Draw stoichiometric
reactants
• Draw reagents
• Balance
!9
MOLECULAR MATERIALS INFORMATICS
The First Step
• Draw product
• Draw stoichiometric
reactants
• Draw reagents
• Balance
!9
MOLECULAR MATERIALS INFORMATICS
The First Step
• Draw product
• Draw stoichiometric
reactants
• Draw reagents
• Balance
!9
MOLECULAR MATERIALS INFORMATICS
The First Step
• Draw product
• Draw stoichiometric
reactants
• Draw reagents
• Balance
!9
MOLECULAR MATERIALS INFORMATICS
Quantities
• Classify primary reactants & waste products
!10
MOLECULAR MATERIALS INFORMATICS
Quantities
• Classify primary reactants & waste products
!10
MOLECULAR MATERIALS INFORMATICS
The Second Step
• Append step
• Draw second product
• Balance: byproducts
• Stoichiometric...
MOLECULAR MATERIALS INFORMATICS
Quantities
• Fill in all available
measurements
• All possible
mappings auto-
calculated
•...
MOLECULAR MATERIALS INFORMATICS
Quantities
• Fill in all available
measurements
• All possible
mappings auto-
calculated
•...
MOLECULAR MATERIALS INFORMATICS
Green Metrics
!13
Process Mass Intensity (PMI) =
mass of all reactants
mass of products
E-...
MOLECULAR MATERIALS INFORMATICS
Green Metrics
• Totals for reactants, products & waste
• For each non-waste product: PMI, ...
MOLECULAR MATERIALS INFORMATICS
Green Solvents
• Environmental data from ACS GCI & GSK
!15
MOLECULAR MATERIALS INFORMATICS
Feedstocks
• Reference collection:
- info about supply chain
- encourage renewable use
• L...
MOLECULAR MATERIALS INFORMATICS
Reaction Transforms
• Provide a pre-curated list of "green"
reaction transforms
• Promote ...
MOLECULAR MATERIALS INFORMATICS
Further Work
• Work in progress: minimum viable product is close
• Experiment definition ex...
Acknowledgments
http://molmatinf.com
http://molsync.com
http://cheminf20.org
!
@aclarkxyz
• Sean Ekins (Green
Solvents)
• ...
Upcoming SlideShare
Loading in …5
×

Building a mobile reaction lab notebook (ACS Dallas 2014)

811
-1

Published on

Describes how a mobile app is being designed to capture chemical reactions at the planning stage, and to record experimental measurements. The app is designed with a data-pure approach to capturing the cheminformatic content of a reaction, which opens the door to a diverse variety of helpful functionality, such as calculation of green chemistry metrics.

Published in: Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
811
On Slideshare
0
From Embeds
0
Number of Embeds
2
Actions
Shares
0
Downloads
5
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Building a mobile reaction lab notebook (ACS Dallas 2014)

  1. 1. Building a mobile reaction lab notebook Alex M. Clark, Ph.D. March 2014 © 2014 Molecular Materials Informatics, Inc.! http://molmatinf.com
  2. 2. MOLECULAR MATERIALS INFORMATICS Electronic Lab Notebooks • Many shapes & sizes: big, small, hosted, desktop, mobile • Domains: chemistry, biology, instrumentation • Many ELNs are generic: functionally equivalent to a Word document • This talk is about chemical reactions !2
  3. 3. MOLECULAR MATERIALS INFORMATICS Data Capture • Reactions normally drawn for chemists… !3 • … rather than computers.
  4. 4. MOLECULAR MATERIALS INFORMATICS Data Capture • Reactions normally drawn for chemists… !3 • … rather than computers.
  5. 5. MOLECULAR MATERIALS INFORMATICS Digitally Friendly !4
  6. 6. MOLECULAR MATERIALS INFORMATICS Digitally Friendly !4 primary! reactant secondary! reactants catalyst solvent intermediate byproducts final! product reagent
  7. 7. MOLECULAR MATERIALS INFORMATICS Functionality • Priorities: 1. computer-friendly datastructures 2. human-friendly workflow • Because people are flexible! We can do better than the tired paper notebook metaphor !5 balancing atom mapping quantity calculation green metrics solvent lookup sustainable feedstocks byproduct datasheets reaction transforms wizards
  8. 8. MOLECULAR MATERIALS INFORMATICS Yield101 • Prior art: designed originally for education • Fancy reaction quantity calculator • Simple & cheap !6 • All quantities mapped to structure: stoichiometry, molecular weight, mass, volume, density, concentration, moles, yield
  9. 9. MOLECULAR MATERIALS INFORMATICS Green Lab Notebook • Under construction as an iOS app (phones & tablets) • Superset of Yield101 core functionality • General purpose reaction lab notebook, with supplementary green chemistry features • Start with experiment drawing… !7
  10. 10. MOLECULAR MATERIALS INFORMATICS A New Experiment • Start with a fresh slate: select the reactant placeholder • Select the draw icon • Sketch the reactant structure • Apply the change: display shows reaction in progress • Note molecular formula & molecular weight !8
  11. 11. MOLECULAR MATERIALS INFORMATICS A New Experiment • Start with a fresh slate: select the reactant placeholder • Select the draw icon • Sketch the reactant structure • Apply the change: display shows reaction in progress • Note molecular formula & molecular weight !8
  12. 12. MOLECULAR MATERIALS INFORMATICS A New Experiment • Start with a fresh slate: select the reactant placeholder • Select the draw icon • Sketch the reactant structure • Apply the change: display shows reaction in progress • Note molecular formula & molecular weight !8
  13. 13. MOLECULAR MATERIALS INFORMATICS A New Experiment • Start with a fresh slate: select the reactant placeholder • Select the draw icon • Sketch the reactant structure • Apply the change: display shows reaction in progress • Note molecular formula & molecular weight !8
  14. 14. MOLECULAR MATERIALS INFORMATICS The First Step • Draw product • Draw stoichiometric reactants • Draw reagents • Balance !9
  15. 15. MOLECULAR MATERIALS INFORMATICS The First Step • Draw product • Draw stoichiometric reactants • Draw reagents • Balance !9
  16. 16. MOLECULAR MATERIALS INFORMATICS The First Step • Draw product • Draw stoichiometric reactants • Draw reagents • Balance !9
  17. 17. MOLECULAR MATERIALS INFORMATICS The First Step • Draw product • Draw stoichiometric reactants • Draw reagents • Balance !9
  18. 18. MOLECULAR MATERIALS INFORMATICS Quantities • Classify primary reactants & waste products !10
  19. 19. MOLECULAR MATERIALS INFORMATICS Quantities • Classify primary reactants & waste products !10
  20. 20. MOLECULAR MATERIALS INFORMATICS The Second Step • Append step • Draw second product • Balance: byproducts • Stoichiometric reagent • For step 2: any non- waste product from step 1 is a primary reactant !11
  21. 21. MOLECULAR MATERIALS INFORMATICS Quantities • Fill in all available measurements • All possible mappings auto- calculated • Cross-fertilised with stoichiometry & molarity • Molecular weight really matters… !12 reactantsproductsreagentsproducts step1step2
  22. 22. MOLECULAR MATERIALS INFORMATICS Quantities • Fill in all available measurements • All possible mappings auto- calculated • Cross-fertilised with stoichiometry & molarity • Molecular weight really matters… !12 reactantsproductsreagentsproducts step1step2
  23. 23. MOLECULAR MATERIALS INFORMATICS Green Metrics !13 Process Mass Intensity (PMI) = mass of all reactants mass of products E-factor = mass of waste mass of products Atom Economy = Σ molecular weight products Σ molecular weight reactants • Trivial calculations… if the information is available.
  24. 24. MOLECULAR MATERIALS INFORMATICS Green Metrics • Totals for reactants, products & waste • For each non-waste product: PMI, E-factor, Atom-E • Always calculated, always recorded… !14
  25. 25. MOLECULAR MATERIALS INFORMATICS Green Solvents • Environmental data from ACS GCI & GSK !15
  26. 26. MOLECULAR MATERIALS INFORMATICS Feedstocks • Reference collection: - info about supply chain - encourage renewable use • Link lab-available quantities to experiment records • Could synchronise with inventory software • Lookup in vendor catalogs... !16 sic
  27. 27. MOLECULAR MATERIALS INFORMATICS Reaction Transforms • Provide a pre-curated list of "green" reaction transforms • Promote user entered experiments into transforms (numbering, clipping) • Associate with: - reagents, catalysts & solvents - stoichiometry & quantities - yield & experimental conditions - literature & green reference data !17 1 2 3 4 5 6 1 2 3 4 5 6
  28. 28. MOLECULAR MATERIALS INFORMATICS Further Work • Work in progress: minimum viable product is close • Experiment definition extensions to include preparation details, free text, spectra, references, pictures, etc. • Synchronisation with centralised databases • Automated structure lookup of problem-compounds: curation required • Curation of sustainable feedstocks & green reaction transforms • Facile promotion of experiment-to-transform: ultra convenient reuse !18
  29. 29. Acknowledgments http://molmatinf.com http://molsync.com http://cheminf20.org ! @aclarkxyz • Sean Ekins (Green Solvents) • Eidogen-Sertanty (Yield101) • Inquiries to info@molmatinf.com

×