Jmol virtual model kit An entirely new way

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

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

Background: “Molecular Origami” • St. Olaf College Chemistry 123 • Start with hand-held models • Develop concepts as needed http: //www. stolaf. edu/people/hansonr/mo/acs 2001

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

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/jmol 10/table/Jcamp. Unknowns. Frames. htm

Spectral Zoo http: //web. centre. edu/muzyka/organic/jmol 10/table/Jcamp. Unknowns. Frames. htm

Spectral Zoo http: //web. centre. edu/muzyka/organic/jmol 10/table/Jcamp. Unknowns. Frames. htm

Standard Jmol Input and Display Capability 3 D Coordinate File MEP Calculated from sdf Data Jmol 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

What’s the logical next step?

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

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

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

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

Why use a model kit? Instructive Illustrates basic geometry Fun! Easy and flexible http: //www. youtube. com/watch? v=38 YKPG 1 r 30 Q

What about virtual models?

What about virtual models? http: //chemapps. stolaf. edu/jmol/docs/examples-12/simple 2. htm

Is there still a need for plastic models?

Jmol Virtual Model Kit

Jmol Virtual Model Kit

Jmol Virtual Model Kit

Jmol Virtual Model Kit

Jmol Virtual Model Kit

Jmol Virtual Model Kit

Jmol Virtual Model Kit

Jmol Virtual Model Kit

Jmol Virtual Model Kit

Jmol Virtual Model Kit

Jmol Virtual Model Kit

Jmol Virtual Model Kit

Jmol Virtual Model Kit set model. Kit. Mode

Jmol Virtual Model Kit load $methylcyclohexane

Jmol Virtual Model Kit load $methylcyclohexane

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

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

Jmol Virtual Model Kit load $methylcyclohexane

Jmol Virtual Model Kit load $methylcyclohexane set picking drag. Minimize

Che. Magic O=Chem VMK http: //chemagic. com/vmk or http: //chemistry. illinoisstate. edu/osrothen/vmk

Che. Magic O=Chem VMK Molecular Editor http: //chemagic. com/vmk or http: //chemistry. illinoisstate. edu/osrothen/vmk

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

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

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

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

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

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

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

Che. Magic O=Chem VMK Model Tools http: //chemagic. com/vmk or http: //chemistry. illinoisstate. edu/osrothen/vmk

nmrdb. org

One more development…

What do you think this displays? <html> <body> <h 3>Acetaminaphen is one of my favorite medications. </h 3> <script type="text/javascript" language="Java. Script" 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. php? model=tylenol&width=300&height=300&inline"> </script>

Jmol molecular “Widget”

Jmol molecular “Widget”

Jmol molecular “Widget”

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?

Thank you!

Background: “Molecular Origami” http: //www. stolaf. edu/people/hansonr/mo/acs 2001/models. htm

Background: “Molecular Origami” http: //www. stolaf. edu/people/hansonr/mo/acs 2001/models. htm

Background: “Molecular Origami” http: //www. stolaf. edu/depts/chemistry/mo/struc/data/f-xef 8 a. mol

Background: “Molecular Origami” http: //www. stolaf. edu/depts/chemistry/mo/struc/data/f-xef 8 a. pdf

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