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

What’s the logical next step?

Why use a model kit?

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

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

Instructive

Why use a model kit?

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?

What about virtual models?

http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.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 modelKitMode

Jmol Virtual Model Kit

load $methylcyclohexane

Jmol Virtual Model Kit

load $methylcyclohexane

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

Jmol Virtual Model Kit

load $methylcyclohexane

Jmol Virtual Model Kit

load $methylcyclohexane

set picking dragMinimize

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

Jmol/JME Information Flow

JmolJME 2D coord

Student

optimizes

draws

+ stereochemistry

Structure Drawing – Comparison of Isomers

http://chemapps.stolaf.edu/jmol/docs/examples-12/isomers.htm

JME

Student

draws

JME

Teacher

expects

Structure Drawing – Comparison of Isomers

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

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://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>

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/acs2001/models.htm

Background: “Molecular Origami”

http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm

Background: “Molecular Origami”

http://www.stolaf.edu/depts/chemistry/mo/struc/data/f-xef8a.mol

Background: “Molecular Origami”

http://www.stolaf.edu/depts/chemistry/mo/struc/data/f-xef8a.pdf

Background: “Molecular Origami”

http://www.stolaf.edu/people/hansonr/mo

150,000,000:1 hydrodroxyapatite model (New Museum of Contemporary Art, New York, NY)