Leveraging Open Notebook Science for solubility andmelting point predictions for optimizing reactions and      recrystalli...
Advantages of ONS for  Undergraduate ResearchGain organization skills and learn howto properly present experimentsReceive ...
Organization and PresentationUpdating the log the day the experiment is performedrequires a student to keep an organized r...
Organization and PresentationTeaches a student how to identify the criticalelements of an experiment           (http://ons...
Correction and InputUsing ONS allows the student to receive neededadvice and guidance from the mentor directly on theexper...
DocumentationAllows a student’s work and contribution to a projectto be documented               (http://onschallenge.wiki...
SolubilityImportant when choosing arecrystallization solventAccurate solubility predictions for acompound allows the optim...
Preferred Solvent         CharacteristicsDoes not react with the compoundbeing recrystallizedHigh solubility at boiling po...
Predicting Solubility with            Abraham Descriptors    Five descriptors for each solute and each solvent    The desc...
Solubility Predictions   Using ONS Webservices, can list the predicted   solubility for a compound   Trans-dibenzalacetone...
Solubility Curves    Using a melting point, temperature dependent    solubility curves are generated    Assumes that at th...
Measuring Solubility     Surprisingly difficult. Must be sure the solution is at     saturation, while avoiding supersatur...
Temperature Controlled Shake       Flask MethodAdd solute to the vials with the solvent and allow toshake in the 25°C wate...
Temperature Controlled Shake       Flask Method   Measure the solubility using HNMR   Need to take two consecutive measure...
Measuring Solubility with NMRCompare integration of solute and solvent peaks insaturated solutions using google app script...
Benefits of Solubility         CurvesThese temperature dependent solubilitycurves allow a solvent with the greatestdiffere...
Example    The solvents used to recrystallize compounds in    organic teaching labs can be improved    Trans-dibenzalaceto...
DibenzalacetoneFirst recrystallized in ethyl acetate in 1906              (Straus and Ecker, Ber. 39, 2988 (1906))Recrysta...
Organic Teaching LabsMany recrystallize in ethyl acetate (http://classes.kvcc.edu/chm230/MIXED%20ALDOL%20CONDENSATION.pdf)...
SmartPhone AppThis app predicts the recrystallization yields of anycompound in different solvents using the solubilitycurv...
SmartPhone AppEnter compound identification (SMILES, CSID,name…etc), and desired parameters                               ...
SmartPhone AppLists solvents and their predicted recrystallizationyield                                  (http://onschalle...
Comparison          Ethyl acetate (predicted yield of 69%) vs ethanol          (predicted yield of 91%)          Ethyl ace...
Solubility at BoilingCannot be too low or an impracticalrecrystallization solventExample: Dibenzalacetone in hexane(predic...
Hexane                                                                                           0.3M(http://showme.physic...
Designing reactions using         solubilityThese solubility tools can be used tochoose a solvent for a reactionFinding a ...
ExampleDerivatives of dibenzalacetone may be synthesizedby altering the aldehyde usedFrom a library of derivatives, the fo...
Search LiteraturePerform a Reaxys© search to determine availability ofsynthesis proceduresNo results
Synthesis Planning    Desire a solvent that the aldehyde is soluble    in, but the product is not    The product was predi...
Synthesis Planning     NaOH is soluble in methanol, so check aldehyde     solubility     Phenanthrene-9-carboxaldehyde    ...
Synthesis PlanningConclusion: Using methanol as thereaction solvent should allow thealdehyde be dissolved into solution, b...
SynthesisCreated an approximately 0.016Msolution of phenanthrene-9-carboxaldehyde in methanolAdded acetone and then a larg...
ProductReaction mixture:           (http://usefulchem.wikispaces.com/EXP286)
Crude ProductFollowing suction filtration: 0.0834 g of yellowcrystals                                   (http://usefulchem...
Recrystallization    Used benzene(http://usefulchem.wikispaces.com/EXP286)    Melting Point: 264-265°
HNMR    Spectrum of product                                                 (http://www.ch                                ...
SummaryOpen Notebook Science providesadvantages to an undergraduateresearcherMeasured and predicted solubilities canbe use...
Further Informationhttp://onschallenge.wikispaces.com/http://usefulchem.wikispaces.com/http://onswebservices.wikispaces.com/
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Open Notebook Science talk at the 2012 ACS

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Video of this presentation can be found here: http://www.youtube.com/watch?v=-rNGkmNTdLc. This talk was given as an oral presentation at the ACS 244th National Meeting held in Philadelphia, PA on August 20, 2012. This talk examined the advantages of being an undergraduate student in a research group using Open Notebook Science. Additionally, this talk examined how to use solubility tools to choose a recrystallization solvent and to plan a reaction synthesis.

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  • http://onschallenge.wikispaces.com/EXP324
  • http://onschallenge.wikispaces.com/EXP321
  • http://onschallenge.wikispaces.com/EXP229http://onschallenge.wikispaces.com/EXP255
  • What makes a solvent optimal: bp, freezing point, etc. Sol at bp (if too low, impractical).
  • http://onschallenge.wikispaces.com/Benzoic+acid+-+AbrahamMake slide clearer
  • http://lxsrv7.oru.edu/~alang/solubility/soltemp.php?csids=555548&cs=0.092&solvent=ethanol&solmp=-114.1&solbp=78.2&limreact=0.3&limprod=0.03http://onschallenge.wikispaces.com/AbrahamDescriptorsModel003Don’t use an ethanol/water mixture, use another solvent Assumption of model: At melting point, solute is micible with solvent
  • Mention NMR method
  • Link to recrystallization page and webservices
  • http://lxsrv7.oru.edu/~alang/solubility/soltemp.php?csids=555548&cs=.624&solvent=ethyl%20acetate&solmp=-83.6&solbp=73.9&limreact=0.3&limprod=0.03State from bp to rtWrite sol at 25C and sol at bp
  • http://usefulchem.wikispaces.com/D-EXP022From a library of derivatives, it was the hop hit for the docking site of taxol
  • http://showme.physics.drexel.edu/onsc/models/solventselector.php?csids=28190813
  • http://usefulchem.wikispaces.com/EXP286
  • Small trace of benzene in nmrBenzene in cdcl315Hz coupling
  • Open Notebook Science talk at the 2012 ACS

    1. 1. Leveraging Open Notebook Science for solubility andmelting point predictions for optimizing reactions and recrystallizations CINF ACS Symposia #244 Philadelphia, PA Matthew McBride Undergraduate Chemistry Major Drexel University Bradley Research Group August 20, 2012
    2. 2. Advantages of ONS for Undergraduate ResearchGain organization skills and learn howto properly present experimentsReceive timely feedback and correctiveinputDocumentation of a student’scontribution to a project
    3. 3. Organization and PresentationUpdating the log the day the experiment is performedrequires a student to keep an organized record of thelab work (http://onschallenge.wikispaces.com/EXP324)Eliminates long term reliance on handwritten notesand allows the log to be recorded when theexperiment is still fresh in the student’s memory
    4. 4. Organization and PresentationTeaches a student how to identify the criticalelements of an experiment (http://onschallenge.wikispaces.com/EXP321)
    5. 5. Correction and InputUsing ONS allows the student to receive neededadvice and guidance from the mentor directly on theexperiment’s page (http://onschallenge.wikispaces.com/EXP255) (http://onschallenge.wikispaces.com/EXP229)Allows the student to understand where an error wasmade and how to avoid repeating the mistake
    6. 6. DocumentationAllows a student’s work and contribution to a projectto be documented (http://onschallenge.wikispaces.com/list+of+experiments)Provides graduate schools with the ability to viewexactly what research an applicant has conducted
    7. 7. SolubilityImportant when choosing arecrystallization solventAccurate solubility predictions for acompound allows the optimal solvent tobe used
    8. 8. Preferred Solvent CharacteristicsDoes not react with the compoundbeing recrystallizedHigh solubility at boiling point, but lowsolubility at room temperatureA boiling point that allows for easydrying of the productMiscibility with water
    9. 9. Predicting Solubility with Abraham Descriptors Five descriptors for each solute and each solvent The descriptors for over 80 solvents, including some ethanol/water mixtures, are known Descriptors for a solute can be experimentally determined by measuring the solubility in 5 solvents Descriptors for a solute can be predicted using AD Model003 Using the solute descriptors, the solubility in any of the solvents with known descriptors can be predicted(http://onschallenge.wikispaces.com/Benzoic+acid+-+Abraham) [William Acree]
    10. 10. Solubility Predictions Using ONS Webservices, can list the predicted solubility for a compound Trans-dibenzalacetone (www.chemspider.com/55 5548)Solvent Model003 AD Measured Experimental BP (M) (M) (M) (°C) (http://showme.physics.drexel.edu/onsc/models/solventselector.php?csids=555548) [Andrew Lang]
    11. 11. Solubility Curves Using a melting point, temperature dependent solubility curves are generated Assumes that at the melting point the compound is miscible with the solvent Solubility in Ethanol (Concentration M vs. Temperature °C)[Andrew Lang] (http://showme.physics.drexel.edu/onsc/models/solventselector.php?csids=555548)
    12. 12. Measuring Solubility Surprisingly difficult. Must be sure the solution is at saturation, while avoiding supersaturated solutions(http://usefulchem.blogspot.com/2010/07/general-transparent-solubility.html)
    13. 13. Temperature Controlled Shake Flask MethodAdd solute to the vials with the solvent and allow toshake in the 25°C water bath (http://onschallenge.wikispaces.com/e xp324)
    14. 14. Temperature Controlled Shake Flask Method Measure the solubility using HNMR Need to take two consecutive measurements without the solubility changing to confirm the solution is saturated(http://onschallenge.wikispaces.com/EXP311)
    15. 15. Measuring Solubility with NMRCompare integration of solute and solvent peaks insaturated solutions using google app scripts 1.5M Saturated solution of dibenzalacetone in THF THF Dibenzalacetone (http://onschallenge.wikispaces.com/EXP308) [Andrew Lang]
    16. 16. Benefits of Solubility CurvesThese temperature dependent solubilitycurves allow a solvent with the greatestdifference between solubility at roomtemperature and at the boiling point tobe usedReduces reliance on only recrystallizingin solvents listed in literatureOptimizes the process of choosing arecrystallization solvent [Andrew Lang]
    17. 17. Example The solvents used to recrystallize compounds in organic teaching labs can be improved Trans-dibenzalacetone(http://showme.physics.drexel.edu/onsc/reactionattempts/advancedsearch.php?compound=&solvent=&reactiontype=&researcher=Matthew+McBride) Aldol condensation between two molecules of benzaldehyde and one molecule of acetone [Andrew Lang]
    18. 18. DibenzalacetoneFirst recrystallized in ethyl acetate in 1906 (Straus and Ecker, Ber. 39, 2988 (1906))Recrystallized in ethyl acetate in Organic Syntheses
    19. 19. Organic Teaching LabsMany recrystallize in ethyl acetate (http://classes.kvcc.edu/chm230/MIXED%20ALDOL%20CONDENSATION.pdf) (http://www.xula.edu/chemistry/documents/orgleclab/Aldol_notes.pdf)Is there a different solvent that could be used?
    20. 20. SmartPhone AppThis app predicts the recrystallization yields of anycompound in different solvents using the solubilitycurves: (http://onschallenge.wikispaces.com/recrystallization)Provides experimental and predicted values formelting point and LogP [Andrew Lang]
    21. 21. SmartPhone AppEnter compound identification (SMILES, CSID,name…etc), and desired parameters (http://onschallenge.wikispaces.com/rec ation) [Andrew Lang]
    22. 22. SmartPhone AppLists solvents and their predicted recrystallizationyield (http://onschallenge.wikispaces.com/recrystalliz ation)Prediction is generated by the temperature [Andrew Lang]
    23. 23. Comparison Ethyl acetate (predicted yield of 69%) vs ethanol (predicted yield of 91%) Ethyl acetate 2.06M 0.62M Ethanol 1.1M 0.09M(http://showme.physics.drexel.edu/onsc/models/solventselector.php?csids=555548)[Andrew Lang]
    24. 24. Solubility at BoilingCannot be too low or an impracticalrecrystallization solventExample: Dibenzalacetone in hexane(predicted yield of 90%)
    25. 25. Hexane 0.3M(http://showme.physics.drexel.edu/onsc/models/solventselector.php?csids=555548) [Andrew Lang] Too insoluble at the boiling point To recrystallize 1 gram of product (4 mmol), would need approximately 13 mL of hexane
    26. 26. Designing reactions using solubilityThese solubility tools can be used tochoose a solvent for a reactionFinding a solvent in which the reactantsare soluble, but the product is insoluble.This allows the product to be recoveredby a simple filtration
    27. 27. ExampleDerivatives of dibenzalacetone may be synthesizedby altering the aldehyde usedFrom a library of derivatives, the following compoundwas the top hit for the docking site of Taxol(http://usefulchem.wikispaces.com/D-EXP022) (http://www.chemspider.com/28190813)Uses phenanthrene-9-carboxaldehyde [Andrew Lang]
    28. 28. Search LiteraturePerform a Reaxys© search to determine availability ofsynthesis proceduresNo results
    29. 29. Synthesis Planning Desire a solvent that the aldehyde is soluble in, but the product is not The product was predicted as having very low solubility (<0.000M) in all solvents NaOH used as the catalyst, so needs to be soluble in the solvent(http://showme.physics.drexel.edu/onsc/models/solventselector.php?csids=28190813) [Andrew Lang]
    30. 30. Synthesis Planning NaOH is soluble in methanol, so check aldehyde solubility Phenanthrene-9-carboxaldehyde (http://www.chemspider.com/708 06) Model003 AD Measured Experimental BPSolvent (M) (M) (M) (°C) (http://showme.physics.drexel.edu/onsc/models/solventselector.php?csids=70806) [Andrew Lang]
    31. 31. Synthesis PlanningConclusion: Using methanol as thereaction solvent should allow thealdehyde be dissolved into solution, butwill cause the product to precipitate
    32. 32. SynthesisCreated an approximately 0.016Msolution of phenanthrene-9-carboxaldehyde in methanolAdded acetone and then a large excessof NaOH (catalyst) to the reactionmixtureStirred mixture without heat over twodays (http://usefulchem.wikispaces.com/EXP286)
    33. 33. ProductReaction mixture: (http://usefulchem.wikispaces.com/EXP286)
    34. 34. Crude ProductFollowing suction filtration: 0.0834 g of yellowcrystals (http://usefulchem.wikispaces.com/EXP 286)
    35. 35. Recrystallization Used benzene(http://usefulchem.wikispaces.com/EXP286) Melting Point: 264-265°
    36. 36. HNMR Spectrum of product (http://www.ch emspider.com/ 28190813) Benzene peak in CDCl3 16Hz Trans Coupling(http://usefulchem.wikispaces.com/EXP286) [Andrew Lang]
    37. 37. SummaryOpen Notebook Science providesadvantages to an undergraduateresearcherMeasured and predicted solubilities canbe used to optimize recrystallizationsPredicted solubilities can be used toplan the synthesis and optimize therecovery of the product
    38. 38. Further Informationhttp://onschallenge.wikispaces.com/http://usefulchem.wikispaces.com/http://onswebservices.wikispaces.com/

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