1. Jmol virtual model kit: An entirely new way to build and explore molecular structures Robert M. Hanson, Otis Rothenberger, Thomas Newton 241 st National Meeting of the American Chemical Society Anaheim, California March 28, 2011

2. Tom Newton Thanks for the great collaboration! Otis Rothenberger

3. The Jmol Project Jmol molecular visualization project Open-source Jmol.sourceforge.net Active user/developer community about 400 “users” about 150 “developers” collectively 23,000 list messages

4. The Jmol Project Jmol molecular visualization project Open-source Jmol.sourceforge.net Active user/developer community about 400 “users” about 150 “developers” collectively 23,000 list messages This means YOU!

5. The Jmol Applet Peter Rose, RCSB http://www.rcsb.org/pdb/explore/jmol.do?structureId=1LDN

6. Alan Hewat, http://icsd.fiz-karlsruhe.de/icsd/

8. Bob Hanson, http://www.stolaf.edu/depts/chemistry/mo/struc/explore.htm

10. The Molecular Workbench Charles Xie, Concord Consortium http://mw.concord.org/modeler/

11. Standard Jmol Input and Display Capability Jmol 3D Coordinate File MDL Molfile mol Protein Data Bank pdb SPARTAN spartan JME Editor jme Structure Data Format sdf MEP Calculated from sdf DataHOMO Calculated from spartan Data Example Coordinate/Data Formats

12. Molecular Orbitals (Including Linear Combinations) http://chemapps.stolaf.edu/jmol/docs/examples-12/motest

13. Molecular Orbitals (Including Linear Combinations) http://chemapps.stolaf.edu/jmol/docs/examples-12/motest

14. What’s the logical next step?

15. A Model Kit http://www.indigo.com/models/molecular-models.html

16. A Model Kit http://www.indigo.com/models/molecular-models.html Instructive

17. A Model Kit http://www.indigo.com/models/molecular-models.html Instructive Basic geometry

18. A Model Kit http://www.indigo.com/models/molecular-models.html Instructive Basic geometry Fun!

19. Jmol Virtual Model Kit

31. set modelKitMode

32. CheMagic O=Chem VMK http://chemagic.com/web_molecules

33. CheMagic O=Chem VMK Structure Drawing http://chemagic.com/web_molecules

34. Jmol/JME Information Flow Jmol (3D)JME (2D) 2D coord Student view optimize compare draws

35. Jmol/JME Information Flow Jmol (3D)JME (2D) SMILES Student draws vs. SMILES compare

36. Jmol/JME Information Flow Jmol (3D)JME (2D) SMILES Student draws Student’s drawn structure compared with key vs. SMILES compare C[C@@H](Br)CCCCC(Br)C

37. Jmol/JME Information Flow Jmol (3D)JME (2D) SMILES Student draws Student’s drawn structure compared with key “Please indicate the stereochemistry.” vs. SMILES compare C[C@@H](Br)CCCCC(Br)C

38. Jmol/JME Information Flow Jmol (3D) Student compare creates 3D or SMILES Jmol can compare natively either SMILES (connections and stereochemistry) or 3D coordinates (connections, stereochemistry, conformation)

39. Jmol Find/Compare Capabilities {*}.find(“SMILES”, SMILES_reference)

40. Jmol Find/Compare Capabilities {*}.find(“SMILES”, SMILES_reference) Do these atoms have the correct connectivity (and absolute stereochemistry)?

41. Jmol Find/Compare Capabilities {*}.find(“SMILES”, SMILES_reference) {*}.find("SMARTS",SMARTS_reference) Do these atoms have the correct connectivity (and absolute stereochemistry)?

42. Jmol Find/Compare Capabilities {*}.find(“SMILES”, SMILES_reference) {*}.find("SMARTS",SMARTS_reference) Do these atoms have the correct connectivity (and absolute stereochemistry)? Does this model contain this substructure (possibly including stereochemistry)?

43. Jmol Find/Compare Capabilities {*}.find(“SMILES”, SMILES_reference) {*}.find("SMARTS",SMARTS_reference) compare({model1}, {model2}, “ISOMER”) Do these atoms have the correct connectivity (and absolute stereochemistry)? Does this model contain this substructure (possibly including stereochemistry)?

44. Jmol Find/Compare Capabilities {*}.find(“SMILES”, SMILES_reference) {*}.find("SMARTS",SMARTS_reference) compare({model1}, {model2}, “ISOMER”) Do these atoms have the correct connectivity (and absolute stereochemistry)? Does this model contain this substructure (possibly including stereochemistry)? Are model1 and model2 identical, enantiomers, diasteriomers, constitutional isomers, or none of the above?

45. Jmol Find/Compare Capabilities {*}.find(“SMILES”, SMILES_reference) {*}.find("SMARTS",SMARTS_reference) compare({model1}, {model2}, “ISOMER”) compare(SMILES1, SMILES2, “ISOMER”) Do these atoms have the correct connectivity (and absolute stereochemistry)? Does this model contain this substructure (possibly including stereochemistry)? Are model1 and model2 identical, enantiomers, diasteriomers, constitutional isomers, or none of the above?

46. Jmol Find/Compare Capabilities {*}.find(“SMILES”, SMILES_reference) {*}.find("SMARTS",SMARTS_reference) compare({model1}, {model2}, “ISOMER”) compare(SMILES1, SMILES2, “ISOMER”) Do these atoms have the correct connectivity (and absolute stereochemistry)? Does this model contain this substructure (possibly including stereochemistry)? Are model1 and model2 identical, enantiomers, diasteriomers, constitutional isomers, or none of the above? Are SMILES1 and SMILES2 identical, enantiomers, diasteriomers, constitutional isomers, or none of the above?

47. CheMagic O=Chem VMK Molecular Editor http://chemagic.com/web_molecules

48. chemical names CAS numbers *SMILES strings IUPAC InChI/InChIKeys NCI/CADD Identifiers CACTVS HASHISY NSC number *molfile /SMILES /names, /iupac_name /cas /inchi, /stdinchi /inchikey, /stdinchikey /ficts, /ficus, /uuuuu /image /file, /sdf /mw, /monoisotopic_mass /formula /twirl, /3d (Just for Fun) /urls (Possibilities) “identifier” “representation” http://cactus.nci.nih.gov/chemical/structure Chemical Identifier Resolver NIH: NCI/CADD Group Web Resource Markus Sitzmann NIH Resolver * Spoken by Jmol

49. Jmol/NIH Information Flow Jmol (3D) Student types “tylenol” This model kit is special!

50. Jmol/NIH Information Flow Jmol (3D) Student types “tylenol” This model kit is special!

51. Jmol/NIH Information Flow Jmol (3D) Student types “tylenol” This model kit is special! NIH Resolver “tylenol”SDF file

52. Jmol/NIH Information Flow Jmol (3D) load “$tylenol” This model kit is special! NIH Resolver “tylenol”SDF file http://cactus.nci.nih.gov/chemical/structure/tylenol/file?format=sdf&get3d=True

53. Jmol/NIH Information Flow Jmol (3D) load “$tylenol” This model kit is special! NIH Resolver “tylenol”SDF file Identifier can be a chemical name, a SMILES string, a CAS registry number, an INCHI key, or many other formats http://cactus.nci.nih.gov/chemical/structure/tylenol/file?format=sdf&get3d=True

54. CheMagic O=Chem VMK Model Tools http://chemagic.com/web_molecules

55. CheMagic O=Chem VMK Social Network http://chemagic.com/web_molecules JME CheMagic nmrdb.org NIST Webbook Jmol PubChem NIH Resolver

56. nmrdb.org

57. One more development…

58. What do you think this displays? Acetaminaphen is one of my favorite medications. <script type="text/javascript" language="JavaScript" src="http://chemagic.com/web_molecules/jmolmodel.aspx?model=tylenol&width=300&height=300">

59. Jmol molecular “Widget”

60. <script type="text/javascript" language="JavaScript" src="http://chemagic.com/web_molecules/jmolmodel.aspx?model=tylenol&width=300&height=300">

61. Thank you!