Building a mobile reaction lab notebook (ACS Dallas 2014)
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This document discusses building a mobile electronic lab notebook focused on chemical reactions called the Green Lab Notebook. It would allow users to draw chemical structures, balance reactions, and calculate quantities, yields, and green metrics. Key features include digitally capturing reaction data, prioritizing computer-friendly data structures and intuitive workflows, and linking to external databases for solvent data, sustainable feedstocks, and curated green reaction transforms. The goal is to facilitate recording, analyzing, and promoting the reuse of experimental reaction data in a sustainable chemistry context.
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Building a mobile reaction lab notebook (ACS Dallas 2014)
- 1. Building a mobile reaction lab notebook Alex M. Clark, Ph.D. March 2014 © 2014 Molecular Materials Informatics, Inc.! http://molmatinf.com
- 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. MOLECULAR MATERIALS INFORMATICS Data Capture • Reactions normally drawn for chemists… !3 • … rather than computers.
- 4. MOLECULAR MATERIALS INFORMATICS Data Capture • Reactions normally drawn for chemists… !3 • … rather than computers.
- 5. MOLECULAR MATERIALS INFORMATICS Digitally Friendly !4
- 6. MOLECULAR MATERIALS INFORMATICS Digitally Friendly !4 primary! reactant secondary! reactants catalyst solvent intermediate byproducts final! product reagent
- 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. 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. 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. 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. 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. 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. 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. MOLECULAR MATERIALS INFORMATICS The First Step • Draw product • Draw stoichiometric reactants • Draw reagents • Balance !9
- 15. MOLECULAR MATERIALS INFORMATICS The First Step • Draw product • Draw stoichiometric reactants • Draw reagents • Balance !9
- 16. MOLECULAR MATERIALS INFORMATICS The First Step • Draw product • Draw stoichiometric reactants • Draw reagents • Balance !9
- 17. MOLECULAR MATERIALS INFORMATICS The First Step • Draw product • Draw stoichiometric reactants • Draw reagents • Balance !9
- 18. MOLECULAR MATERIALS INFORMATICS Quantities • Classify primary reactants & waste products !10
- 19. MOLECULAR MATERIALS INFORMATICS Quantities • Classify primary reactants & waste products !10
- 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. 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. 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. 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. 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. MOLECULAR MATERIALS INFORMATICS Green Solvents • Environmental data from ACS GCI & GSK !15
- 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. 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. 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. Acknowledgments http://molmatinf.com http://molsync.com http://cheminf20.org ! @aclarkxyz • Sean Ekins (Green Solvents) • Eidogen-Sertanty (Yield101) • Inquiries to info@molmatinf.com