1. Jmol virtual model kit: An entirely new way to build and explore molecular structures Robert M. Hanson Lexington Section, American Chemical Society Centre College, Danville, Kentucky Monday, Oct. 17, 2011

2. Tom Newton, U. So. Maine. Thanks for the great collaboration! Otis Rothenberger, Ill. State Markus Sitzmann, NCI-NIH

3. Executive Summary The Jmol project My interest in visualization A few examples Model kits – physical vs. virtual

4. The Jmol Project Jmol molecular visualization project Open-source (LGPL license allows limited commercialization) http://jmol.sourceforge.net Active user/developer community about 400 “users” about 150 “developers” collectively 23,000 list messages

5. St. Olaf College Chemistry 123 Start with hand-held models Develop concepts as needed Background: “Molecular Origami” http://www.stolaf.edu/people/hansonr/mo/acs2001

6. Background: “Molecular Origami” http://www.stolaf.edu/people/hansonr/mo normal quartz

7. http://www.stolaf.edu/depts/chemistry/mo/struc/explore.htm

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

9. Spectral Zoo http://web.centre.edu/muzyka/organic/jmol10/table/JcampUnknownsFrames.htm

10. Spectral Zoo http://web.centre.edu/muzyka/organic/jmol10/table/JcampUnknownsFrames.htm

11. Spectral Zoo http://web.centre.edu/muzyka/organic/jmol10/table/JcampUnknownsFrames.htm

12. Standard Jmol Input and Display Capability Jmol 3D Coordinate File MEP Calculated from sdf DataHOMO Calculated from spartan Data

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

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

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

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

17. What’s the logical next step?

18. Why use a model kit? http://www.indigo.com/models/molecular-models.html

19. Instructive Why use a model kit?

20. http://www.indigo.com/models/molecular-models.html Instructive Illustrates basic geometry Why use a model kit?

21. http://www.indigo.com/models/molecular-models.html Instructive Illustrates basic geometry Fun! Why use a model kit?

22. http://www.youtube.com/watch?v=38YKPG1r30Q Instructive Illustrates basic geometry Fun! Easy and flexible Why use a model kit?

23. What about virtual models?

24. http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm

25. Is there still a need for plastic models?

26. Jmol Virtual Model Kit

38. set modelKitMode

39. Jmol Virtual Model Kit load $methylcyclohexane

40. Jmol Virtual Model Kit load $methylcyclohexane

41. chemical names CAS numbers *molfile *SMILES strings IUPAC InChI/InChIKeys NCI/CADD Identifiers CACTVS HASHISY NSC number /cas /ficts, /ficus, /uuuuu /formula /inchi, /stdinchi /inchikey, /stdinchikey /mw /names, /iupac_name /SMILES /file, /sdf /image /urls (Possibilities) “identifier” “representation” http://cactus.nci.nih.gov/chemical/structure Chemical Identifier Resolver NIH: NCI/CADD Group Web Resource Markus Sitzmann NIH Resolver * From a Jmol model * Returned to Jmol

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

43. Jmol Virtual Model Kit load $methylcyclohexane

44. Jmol Virtual Model Kit load $methylcyclohexane set picking dragMinimize

45. CheMagic O=Chem VMK http://chemagic.com/vmkhttp://chemagic.com/vmk or http://chemistry.illinoisstate.edu/osrothen/vmkhttp://chemistry.illinoisstate.edu/osrothen/vmk

46. CheMagic O=Chem VMK Molecular Editor http://chemagic.com/vmkhttp://chemagic.com/vmk or http://chemistry.illinoisstate.edu/osrothen/vmkhttp://chemistry.illinoisstate.edu/osrothen/vmk

47. CheMagic O=Chem VMK Structure Drawing JME applet by Peter Ertl, Novartis, Basel, Switzerland http://chemagic.com/vmkhttp://chemagic.com/vmk or http://chemistry.illinoisstate.edu/osrothen/vmkhttp://chemistry.illinoisstate.edu/osrothen/vmk

48. Jmol/JME Information Flow JmolJME 2D coord Student optimizes draws + stereochemistry

49. Structure Drawing – Comparison of Isomers http://chemapps.stolaf.edu/jmol/docs/examples-12/isomers.htm

50. JME Student draws JME Teacher expects Structure Drawing – Comparison of Isomers

51. Jmol JME SMILES string Student draws JME Teacher expects SMILES string Structure Drawing – Comparison of Isomers CCC(Br)CC[C@@H](Br)CC compares

52. Jmol JME SMILES string Student compares draws JME Teacher expects SMILES string Please indicate the stereochemistry CCC(Br)CC[C@@H](Br)CC Structure Drawing – Comparison of Isomers

53. Jmol (3D) Student compare creates 3D or SMILES Jmol can compare natively both SMILES (connections and stereochemistry) and 3D coordinates (connections, stereochemistry, conformation) 2D and 3D Comparison of Isomers

54. CheMagic O=Chem VMK Model Tools http://chemagic.com/vmkhttp://chemagic.com/vmk or http://chemistry.illinoisstate.edu/osrothen/vmkhttp://chemistry.illinoisstate.edu/osrothen/vmk

55. nmrdb.org

56. One more development…

57. What do you think this displays? Acetaminaphen is one of my favorite medications. <script type="text/javascript" language="JavaScript" src=http://chemapps.stolaf.edu/mol/jmol.php?model=tylenol&width=300&height=300&inlinehttp://chemapps.stolaf.edu/mol/jmol.php?model=tylenol&width=300&height=300&inline >

59. Jmol molecular “Widget” <script type="text/javascript” src="http://chemapps.stolaf.edu/jmol/jmol.php? model=tylenol&width=300&height=300&inline">

60. Jmol molecular “Widget”

63. What do you think? Are virtual models an adequate substitute for physical models? Do they serve the same or different purpose? Should organic chemistry students be required to purchase plastic molecular model kits?

64. Thank you!

65. Background: “Molecular Origami” http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm

66. Background: “Molecular Origami” http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm

67. Background: “Molecular Origami” http://www.stolaf.edu/depts/chemistry/mo/struc/data/f-xef8a.mol

68. Background: “Molecular Origami” http://www.stolaf.edu/depts/chemistry/mo/struc/data/f-xef8a.pdf

69. Background: “Molecular Origami” http://www.stolaf.edu/people/hansonr/mo 150,000,000:1 hydrodroxyapatite model (New Museum of Contemporary Art, New York, NY)