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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
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Tom Newton, U. So. Maine. Thanks for the great collaboration! Otis Rothenberger, Ill. State Markus Sitzmann, NCI-NIH
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Executive Summary The Jmol project My interest in visualization A few examples Model kits – physical vs. virtual
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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
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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
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Background: “Molecular Origami” http://www.stolaf.edu/people/hansonr/mo normal quartz
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http://www.stolaf.edu/depts/chemistry/mo/struc/explore.htm
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Bob Hanson, http://www.stolaf.edu/depts/chemistry/mo/struc/explore.htmhttp://www.stolaf.edu/depts/chemistry/mo/struc/explore.htm
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Spectral Zoo http://web.centre.edu/muzyka/organic/jmol10/table/JcampUnknownsFrames.htm
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Spectral Zoo http://web.centre.edu/muzyka/organic/jmol10/table/JcampUnknownsFrames.htm
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Spectral Zoo http://web.centre.edu/muzyka/organic/jmol10/table/JcampUnknownsFrames.htm
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Standard Jmol Input and Display Capability Jmol 3D Coordinate File MEP Calculated from sdf DataHOMO Calculated from spartan Data
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Molecular Orbitals (Including Linear Combinations) http://chemapps.stolaf.edu/jmol/docs/examples-12/motest
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Molecular Orbitals (Including Linear Combinations) http://chemapps.stolaf.edu/jmol/docs/examples-12/motest
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Molecular Orbitals (Including Linear Combinations) http://chemapps.stolaf.edu/jmol/docs/examples-12/motest
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Molecular Orbitals (Including Linear Combinations) http://chemapps.stolaf.edu/jmol/docs/examples-12/motest
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What’s the logical next step?
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Why use a model kit? http://www.indigo.com/models/molecular-models.html
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Instructive Why use a model kit?
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http://www.indigo.com/models/molecular-models.html Instructive Illustrates basic geometry Why use a model kit?
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http://www.indigo.com/models/molecular-models.html Instructive Illustrates basic geometry Fun! Why use a model kit?
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http://www.youtube.com/watch?v=38YKPG1r30Q Instructive Illustrates basic geometry Fun! Easy and flexible Why use a model kit?
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What about virtual models?
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http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm
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Is there still a need for plastic models?
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Jmol Virtual Model Kit
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set modelKitMode
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Jmol Virtual Model Kit load $methylcyclohexane
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Jmol Virtual Model Kit load $methylcyclohexane
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chemical names CAS numbers *molfile *SMILES strings IUPAC InChI/InChIKeys NCI/CADD Identifiers CACTVS HASHISY NSC number /cas /ficts, /ficus, /uuuuu /formula /inchi, /stdinchi /inchikey, /stdinchikey /mw /names, /iupac_name /SMILES /file, /sdf /image /urls (Possibilities) “identifier” “representation” http://cactus.nci.nih.gov/chemical/structure Chemical Identifier Resolver NIH: NCI/CADD Group Web Resource Markus Sitzmann NIH Resolver * From a Jmol model * Returned to Jmol
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Jmol/NIH Information Flow Jmol (3D) load “$tylenol” NIH Resolver “tylenol”SDF file http://cactus.nci.nih.gov/chemical/structure/tylenol/file?format=sdf&get3d=True
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Jmol Virtual Model Kit load $methylcyclohexane
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Jmol Virtual Model Kit load $methylcyclohexane set picking dragMinimize
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CheMagic O=Chem VMK http://chemagic.com/vmkhttp://chemagic.com/vmk or http://chemistry.illinoisstate.edu/osrothen/vmkhttp://chemistry.illinoisstate.edu/osrothen/vmk
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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
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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
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Jmol/JME Information Flow JmolJME 2D coord Student optimizes draws + stereochemistry
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Structure Drawing – Comparison of Isomers http://chemapps.stolaf.edu/jmol/docs/examples-12/isomers.htm
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JME Student draws JME Teacher expects Structure Drawing – Comparison of Isomers
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Jmol JME SMILES string Student draws JME Teacher expects SMILES string Structure Drawing – Comparison of Isomers CCC(Br)CC[C@@H](Br)CC compares
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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
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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
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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
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nmrdb.org
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One more development…
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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 >
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Jmol molecular “Widget” <script type="text/javascript” src="http://chemapps.stolaf.edu/jmol/jmol.php? model=tylenol&width=300&height=300&inline">
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Jmol molecular “Widget”
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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?
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Thank you!
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Background: “Molecular Origami” http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm
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Background: “Molecular Origami” http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm
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Background: “Molecular Origami” http://www.stolaf.edu/depts/chemistry/mo/struc/data/f-xef8a.mol
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Background: “Molecular Origami” http://www.stolaf.edu/depts/chemistry/mo/struc/data/f-xef8a.pdf
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Background: “Molecular Origami” http://www.stolaf.edu/people/hansonr/mo 150,000,000:1 hydrodroxyapatite model (New Museum of Contemporary Art, New York, NY)
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