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

Tom Newton Thanks for the great collaboration! Otis Rothenberger

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

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!

The Jmol Applet Peter Rose, RCSB

Alan Hewat,

Bob Hanson,

The Molecular Workbench Charles Xie, Concord Consortium

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

Molecular Orbitals (Including Linear Combinations)

Molecular Orbitals (Including Linear Combinations)

What’s the logical next step?

A Model Kit

A Model Kit Instructive

A Model Kit Instructive Basic geometry

A Model Kit Instructive Basic geometry Fun!

Jmol Virtual Model Kit

set modelKitMode

CheMagic O=Chem VMK

CheMagic O=Chem VMK Structure Drawing

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

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

Jmol/JME Information Flow Jmol (3D)JME (2D) SMILES Student draws Student’s drawn structure compared with key vs. SMILES compare

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

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)

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

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

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

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)?

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)?

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?

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?

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?

CheMagic O=Chem VMK Molecular Editor

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” Chemical Identifier Resolver NIH: NCI/CADD Group Web Resource Markus Sitzmann NIH Resolver * Spoken by Jmol

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

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

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

Jmol/NIH Information Flow Jmol (3D) load “$tylenol” This model kit is special! NIH Resolver “tylenol”SDF file

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

CheMagic O=Chem VMK Model Tools

CheMagic O=Chem VMK Social Network JME CheMagic nmrdb.org NIST Webbook Jmol PubChem NIH Resolver

nmrdb.org

One more development…

What do you think this displays? Acetaminaphen is one of my favorite medications. <script type="text/javascript" language="JavaScript" src="

Jmol molecular “Widget”

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Thank you!