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Chemical structure
diagrams, reactions and
data: anytime, anywhere

                                               Dr. Alex M. Clark
                                                     August 2012



© 2012 Molecular Materials Informatics, Inc.
  http://molmatinf.com
                              1
Apps
• Already making an impact on education

• Plenty of content consumption - apps have
  always been good for that

• But what about content creation?

• Much harder, especially for chemical
  structures
Draw a molecule
• Being able to specify a molecule opens doors




Is it valid?                        Present it




       Obtain     Lookup in      Share it
     properties    catalog
+
             MolPrime


                main menu pic




• Available for iOS, with Android coming soon
Sketching
• Sketcher is designed for
  optimal use on small screens

• Gestures, tools, templates: for
  drawing perfect structures, with
  minimum interaction

• Basic primitives for molecular
  diagram sketching, Journal of
  Cheminformatics, 2:8 (2010)
Validity
• Property calculation includes
  valence checking

• Identify basic problems with
  structures

• Drawing errors or chemistry
  misunderstandings lead to
  invalid oxidation states
Properties
• Scalar properties can be derived from the structure...

                      • Simple properties are calculated on the
                        device:

                        - molecular formula & weight
                        - atom-type counts
                        - rotatable bonds

                      • Detailed calculations via webservice:

                        - log P
                        - molar refractivity
                        - topological polar surface area
Stereochemistry

• Webservice for calculating
  stereochemistry:

 - chirality (R/S)
 - double bonds (E/Z)

• Use the app to draw the
  molecule and obtain the correct
  answer
Tautomers
• Webservice can calculate tautomers and provide an
  interconversion graph




• App allows navigation through
  tautomer space
Mass spectroscopy




• Can calculate the isotopic mass distribution,
  and exact mass, based on the structure

• Helps with assigning mass spectra
Lookup online




• Many ways to lookup molecular structure in online:
  e.g. Open with the ChemSpider Mobile app

• Can also search SPRESI, Mobile Reagents,
  PubChem, ChEBI, eMolecules
Presentation
 • Can copy bitmap to clipboard: paste into iWork

 • Or create vector graphics (SVG, EPS, Word/Excel)




Vector                                          Bitmap
Sharing: Email

                • Initiate an
                  email, with an
                  image, source
                  data...



• Recipient can view the picture...

• ... and open the data: with an app, or any other
  platform software.
Sharing: Web
                   • Upload to molsync.com



                   • View public link


• Can share the link with anyone,
  e.g. via social networks

• Can download the structure in
  many formats, including graphics
Twitter
• Can tweet from app using
  iOS Twitter integration

• Uploads molecule to website

• Includes the link within the
  tweet

• Link provides viewing and
  access to the data
See Also                      http://molmatinf.com/products.html

                       1.5
    Mobile Molecular    Open Drug Discovery
    DataSheet (MMDS)         Teams (ODDT)
                                   with Collaborations in Chemistry



    MolSync                  ChemSpider Mobile
                                  with Royal Society of Chemistry




    SAR Table                       SPRESI mobile
                                                  with InfoChem




    MolPrime                           Reaction101
                                            with Eidogen-Sertanty




     Green Solvents                            Yield101
                                           with Eidogen-Sertanty
Conclusion
• Numerous ways to teach chemistry,
  using molecular structures

• Useful pedagogical tools already
  available, starting with structure drawing

• This is just the
                               http://molmatinf.com
  beginning... so many         http://molsync.com
  more ideas to explore.       http://cheminf20.org


                               @aclarkxyz
                     17

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Alex M. Clark, Chemical Education, ACS 2012 Philadelphia

  • 1. Chemical structure diagrams, reactions and data: anytime, anywhere Dr. Alex M. Clark August 2012 © 2012 Molecular Materials Informatics, Inc. http://molmatinf.com 1
  • 2. Apps • Already making an impact on education • Plenty of content consumption - apps have always been good for that • But what about content creation? • Much harder, especially for chemical structures
  • 3. Draw a molecule • Being able to specify a molecule opens doors Is it valid? Present it Obtain Lookup in Share it properties catalog
  • 4. + MolPrime main menu pic • Available for iOS, with Android coming soon
  • 5. Sketching • Sketcher is designed for optimal use on small screens • Gestures, tools, templates: for drawing perfect structures, with minimum interaction • Basic primitives for molecular diagram sketching, Journal of Cheminformatics, 2:8 (2010)
  • 6. Validity • Property calculation includes valence checking • Identify basic problems with structures • Drawing errors or chemistry misunderstandings lead to invalid oxidation states
  • 7. Properties • Scalar properties can be derived from the structure... • Simple properties are calculated on the device: - molecular formula & weight - atom-type counts - rotatable bonds • Detailed calculations via webservice: - log P - molar refractivity - topological polar surface area
  • 8. Stereochemistry • Webservice for calculating stereochemistry: - chirality (R/S) - double bonds (E/Z) • Use the app to draw the molecule and obtain the correct answer
  • 9. Tautomers • Webservice can calculate tautomers and provide an interconversion graph • App allows navigation through tautomer space
  • 10. Mass spectroscopy • Can calculate the isotopic mass distribution, and exact mass, based on the structure • Helps with assigning mass spectra
  • 11. Lookup online • Many ways to lookup molecular structure in online: e.g. Open with the ChemSpider Mobile app • Can also search SPRESI, Mobile Reagents, PubChem, ChEBI, eMolecules
  • 12. Presentation • Can copy bitmap to clipboard: paste into iWork • Or create vector graphics (SVG, EPS, Word/Excel) Vector Bitmap
  • 13. Sharing: Email • Initiate an email, with an image, source data... • Recipient can view the picture... • ... and open the data: with an app, or any other platform software.
  • 14. Sharing: Web • Upload to molsync.com • View public link • Can share the link with anyone, e.g. via social networks • Can download the structure in many formats, including graphics
  • 15. Twitter • Can tweet from app using iOS Twitter integration • Uploads molecule to website • Includes the link within the tweet • Link provides viewing and access to the data
  • 16. See Also http://molmatinf.com/products.html 1.5 Mobile Molecular Open Drug Discovery DataSheet (MMDS) Teams (ODDT) with Collaborations in Chemistry MolSync ChemSpider Mobile with Royal Society of Chemistry SAR Table SPRESI mobile with InfoChem MolPrime Reaction101 with Eidogen-Sertanty Green Solvents Yield101 with Eidogen-Sertanty
  • 17. Conclusion • Numerous ways to teach chemistry, using molecular structures • Useful pedagogical tools already available, starting with structure drawing • This is just the http://molmatinf.com beginning... so many http://molsync.com more ideas to explore. http://cheminf20.org @aclarkxyz 17