Post on 19-Dec-2015
Jmol virtual model kit: An entirely new way to build and explore molecular structures
Robert M. HansonLexington Section, American Chemical Society
Centre College, Danville, KentuckyMonday, Oct. 17, 2011
Tom Newton,U. So. Maine.
Thanks for the greatcollaboration!
Otis Rothenberger,Ill. State
MarkusSitzmann,NCI-NIH
Executive Summary
• The Jmol project• My interest in visualization• A few examples• Model kits – physical vs. virtual
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
• 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
Background: “Molecular Origami”
http://www.stolaf.edu/people/hansonr/mo
normal quartz
http://www.stolaf.edu/depts/chemistry/mo/struc/explore.htm
Bob Hanson, http://www.stolaf.edu/depts/chemistry/mo/struc/explore.htm
Spectral Zoo
http://web.centre.edu/muzyka/organic/jmol10/table/JcampUnknownsFrames.htm
Spectral Zoo
http://web.centre.edu/muzyka/organic/jmol10/table/JcampUnknownsFrames.htm
Spectral Zoo
http://web.centre.edu/muzyka/organic/jmol10/table/JcampUnknownsFrames.htm
Standard Jmol Input and Display Capability
Jmol3D
CoordinateFile
MEP Calculated from sdf Data HOMO Calculated from spartan Data
Molecular Orbitals (Including Linear Combinations)
http://chemapps.stolaf.edu/jmol/docs/examples-12/motest
Molecular Orbitals (Including Linear Combinations)
http://chemapps.stolaf.edu/jmol/docs/examples-12/motest
Molecular Orbitals (Including Linear Combinations)
http://chemapps.stolaf.edu/jmol/docs/examples-12/motest
Molecular Orbitals (Including Linear Combinations)
http://chemapps.stolaf.edu/jmol/docs/examples-12/motest
http://www.indigo.com/models/molecular-models.html
InstructiveIllustrates basic geometry
Why use a model kit?
http://www.indigo.com/models/molecular-models.html
InstructiveIllustrates basic geometryFun!
Why use a model kit?
http://www.youtube.com/watch?v=38YKPG1r30Q
InstructiveIllustrates basic geometryFun!Easy and flexible
Why use a model kit?
What about virtual models?
http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm
chemical namesCAS numbers
*molfile*SMILES strings
IUPAC InChI/InChIKeysNCI/CADD Identifiers
CACTVS HASHISYNSC 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 ResolverNIH: NCI/CADD Group Web Resource
Markus Sitzmann
NIH Resolver
* From a Jmol model
* Returned to Jmol
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
CheMagic O=Chem VMK
http://chemagic.com/vmk or http://chemistry.illinoisstate.edu/osrothen/vmk
CheMagic O=Chem VMKMolecular Editor
http://chemagic.com/vmk or http://chemistry.illinoisstate.edu/osrothen/vmk
CheMagic O=Chem VMKStructure Drawing
JME applet by Peter Ertl, Novartis, Basel, Switzerland
http://chemagic.com/vmk or http://chemistry.illinoisstate.edu/osrothen/vmk
Structure Drawing – Comparison of Isomers
http://chemapps.stolaf.edu/jmol/docs/examples-12/isomers.htm
Jmol
JME
SMILES string
Student
draws
JME
Teacher
expects
SMILES string
Structure Drawing – Comparison of Isomers
CCC(Br)C C[C@@H](Br)CC
compares
Jmol
JME
SMILES string
Student
compares
draws
JME
Teacher
expects
SMILES string
Please indicate the stereochemistry
CCC(Br)C C[C@@H](Br)CC
Structure Drawing – Comparison of Isomers
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
CheMagic O=Chem VMKModel Tools
http://chemagic.com/vmk or http://chemistry.illinoisstate.edu/osrothen/vmk
What do you think this displays?
<html><body><h3>Acetaminaphen is one of my favorite medications.</h3><br /><script type="text/javascript" language="JavaScript"
src=http://chemapps.stolaf.edu/mol/jmol.php?model=tylenol&width=300&height=300&inline
></script></body></html>
Jmol molecular “Widget”
<script type="text/javascript”
src="http://chemapps.stolaf.edu/jmol/jmol.php? model=tylenol&width=300&height=300&inline">
</script>
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?