building a mobile reaction lab notebook (acs dallas 2014)
DESCRIPTION
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.TRANSCRIPT
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Building a mobile reaction lab notebook
Alex M. Clark, Ph.D.
March 2014
© 2014 Molecular Materials Informatics, Inc.! http://molmatinf.com
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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
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MOLECULAR MATERIALS INFORMATICS
Data Capture• Reactions normally drawn for chemists…
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• … rather than computers.
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MOLECULAR MATERIALS INFORMATICS
Data Capture• Reactions normally drawn for chemists…
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• … rather than computers.
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MOLECULAR MATERIALS INFORMATICS
Digitally Friendly!4
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MOLECULAR MATERIALS INFORMATICS
Digitally Friendly!4
primary!reactant
secondary!reactants
catalyst
solvent
intermediate
byproducts
final!product
reagent
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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
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balancing atom mapping
quantity calculation
green metrics
solvent lookup
sustainable feedstocks byproduct datasheets
reaction transforms wizards
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MOLECULAR MATERIALS INFORMATICS
Yield101• Prior art: designed
originally for education
• Fancy reaction quantity calculator
• Simple & cheap
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• All quantities mapped to structure: stoichiometry, molecular weight, mass, volume, density, concentration, moles, yield
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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…
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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
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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
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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
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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
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MOLECULAR MATERIALS INFORMATICS
The First Step
• Draw product
• Draw stoichiometric reactants
• Draw reagents
• Balance
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MOLECULAR MATERIALS INFORMATICS
The First Step
• Draw product
• Draw stoichiometric reactants
• Draw reagents
• Balance
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MOLECULAR MATERIALS INFORMATICS
The First Step
• Draw product
• Draw stoichiometric reactants
• Draw reagents
• Balance
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MOLECULAR MATERIALS INFORMATICS
The First Step
• Draw product
• Draw stoichiometric reactants
• Draw reagents
• Balance
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MOLECULAR MATERIALS INFORMATICS
Quantities
• Classify primary reactants & waste products
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MOLECULAR MATERIALS INFORMATICS
Quantities
• Classify primary reactants & waste products
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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
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MOLECULAR MATERIALS INFORMATICS
Quantities• Fill in all available
measurements
• All possible mappings auto-calculated
• Cross-fertilised with stoichiometry & molarity
• Molecular weight really matters…
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reac
tant
spr
oduc
tsre
agen
tspr
oduc
tsst
ep 1
step
2
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MOLECULAR MATERIALS INFORMATICS
Quantities• Fill in all available
measurements
• All possible mappings auto-calculated
• Cross-fertilised with stoichiometry & molarity
• Molecular weight really matters…
!12
reac
tant
spr
oduc
tsre
agen
tspr
oduc
tsst
ep 1
step
2
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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 productsΣ molecular weight reactants
• Trivial calculations… if the information is available.
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MOLECULAR MATERIALS INFORMATICS
Green Metrics
• Totals for reactants, products & waste • For each non-waste product: PMI, E-factor, Atom-E • Always calculated, always recorded…
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MOLECULAR MATERIALS INFORMATICS
Green Solvents
• Environmental data from ACS GCI & GSK
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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...
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sic
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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
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1 2 3 45
6 1 2 3
4
56
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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
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Acknowledgments
http://molmatinf.com http://molsync.com http://cheminf20.org !
@aclarkxyz
• Sean Ekins (Green Solvents)
• Eidogen-Sertanty (Yield101)
• Inquiries to [email protected]