Jmol virtual model kit: An entirely new way to build and explore molecular structures

Robert M. Hanson, Otis Rothenberger, Thomas Newton241st National Meeting of the American Chemical Society

Anaheim, CaliforniaMarch 28, 2011

Tom Newton

Thanks for the greatcollaboration!

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 http://www.rcsb.org/pdb/explore/jmol.do?structureId=1LDN

Alan Hewat, http://icsd.fiz-karlsruhe.de/icsd/

Alan Hewat, http://icsd.fiz-karlsruhe.de/icsd/

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

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

The Molecular Workbench

Charles Xie, Concord Consortium http://mw.concord.org/modeler/

Standard Jmol Input and Display Capability

Jmol3D

CoordinateFile

MDL Molfilemol

Protein Data Bankpdb

SPARTANspartan

JME Editorjme

Structure Data Formatsdf

MEP Calculated from sdf Data HOMO Calculated from spartan Data

Example Coordinate/Data Formats

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?

A Model Kit

http://www.indigo.com/models/molecular-models.html

A Model Kit

http://www.indigo.com/models/molecular-models.html

Instructive

A Model Kit

http://www.indigo.com/models/molecular-models.html

InstructiveBasic geometry

A Model Kit

http://www.indigo.com/models/molecular-models.html

InstructiveBasic geometryFun!

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 modelKitMode

CheMagic O=Chem VMK

http://chemagic.com/web_molecules

CheMagic O=Chem VMKStructure Drawing

http://chemagic.com/web_molecules

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

C[C@@H](Br)CCCCC(Br)C

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

C[C@@H](Br)CCCCC(Br)C

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 VMKMolecular Editor

http://chemagic.com/web_molecules

chemical namesCAS numbers

*SMILES stringsIUPAC InChI/InChIKeys

NCI/CADD IdentifiersCACTVS 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”

http://cactus.nci.nih.gov/chemical/structure

Chemical Identifier ResolverNIH: 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

http://cactus.nci.nih.gov/chemical/structure/tylenol/file?format=sdf&get3d=True

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

http://cactus.nci.nih.gov/chemical/structure/tylenol/file?format=sdf&get3d=True

CheMagic O=Chem VMKModel Tools

http://chemagic.com/web_molecules

CheMagic O=Chem VMK Social Network

http://chemagic.com/web_molecules

JME

CheMagic

nmrdb.orgNIST Webbook

Jmol

PubChem

NIH Resolver

nmrdb.org

One more development…

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://chemagic.com/web_molecules/jmolmodel.aspx?model=tylenol&width=300&height=300">

</script></body></html>

Jmol molecular “Widget”

Jmol molecular “Widget”

<script type="text/javascript" language="JavaScript"

src="http://chemagic.com/web_molecules/jmolmodel.aspx?model=tylenol&width=300&height=300">

</script>

Thank you!