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.

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