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Interactive OChem Structures and Animations

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Interactive OChem Structures and Animations
by Carl LeBlond - Thursday, October 16, 2014, 9:20 PM

I have developed quite a few interactive demonstrations and animations for my online courses over the past two years.  Unfortunately most of it is buried in glossaries or various deep in course pages on EasyOChem and I forget about them.  In an effort to make them more accessible I took an hour and compiled links to all of them.  Most of them are 3D JMOL or JSMOL structures and animations.  There's also a few animated GIF's I did with GIMP.  These are all in the EasyOChem Glossary and Organic Chemistry I course.

EasyOChem Glossary

boat (cyclohexane conformation)

- 3D JSMOL boat cyclohexane

chair (cyclohexane conformation)

- Interactive ring flip occuring (JSMol)


- 3D JSMol structure of diamond


- interactive Marvin View 3D structures of diasteromers.

Diels Alder Reaction

- animated GIF showing bond formation and breaking


-interactive JmoL demosration of enantiomers in mirror

Fischer Projections

- interactive JMOL demonstration of enantiomers in mirror


- JSMol

half chair (cyclohexane conformation)

- JSMOL structure

Hydrogen bond

- JSMOL - collection of water molecules hydrogen bonding


- interactive JMOL applet illustrating hyperconjugation in cations and alkenes.


- JMOL applet in which user can visualize any 2nd row orbitals.

R/S Nomenclature

- Interactive JSMOL and inline questions illustrating R/S stereocemistry

Twist boat (cyclohexane conformation)

- JSMol interactive 3D

Walden Inversion

- animated GIF of SN2 reaction

Organic Chemistry I

Developing your Chemical Intuition!

- JMOL applets showing ethene at different levels of abstraction


Electron Configurations and Atomic Orbitals

- JMOL applet showing 2nd row orbitals

Intro to Molecular Orbital (MO) Theory Page

- JMOL's showing 3D bonding and antibonding molecular orbitals for σ and π bonds


- interactive inline questions.

Resonance Between Three Atoms

- interactive inline questions

Resonance in Conjugated Systems

- 3D JSMOL Molecular Orbitals of butadiene

Electron Sources

- 3D JSMOL Molecular Orbitals

Conformations of Acyclic Alkanes

- interactive JMOL script - Show dihedral angle and different conformations of butane

Conformations of Cyclic Alkanes

- 3D interactive JSMOl cyclopropane, cyclobutane, cylopentane, cyclohexane and more.

Potential Energy Surface of the Conformations of Butane

- 3D butane potential energy surface animation (JMOL/FLOT)

Conformational Mobility of Cycohexanes

- 3D cyclohexane potential energy surface animation (JMOL/FLOT)

Conformational Analysis of Substituted Cyclohexanes

- JSMOL demo of 1,3-diaxial strain


- 3D JMOL applets users can show and hide molecular orbitals important in hyperconjugation

Chirality or Handedness.

- interactive 3D JMOL Applet with enantiomers synchronized in mirror plane.


- interactive 3D JMOL Applet with enantiomers synchronized in mirror plane.

R/S Determination

- interactive 3D JSMOL tutorial on determining R/S stereochemistry

Meso Compounds

- 3D JSMOl meso compund showing plane of symmetry

Nucleophilic Substitution: SN1 and SN2 Mechanisms

- 3D JMOL animation of SN2 mechanism

Diels Alder Reaction

- 3D JMOL animated Diels Alder reaction

Diels Alder - Endo vs Exo

- 3D JMOL animations illustrating the endo and exo product formation

Benzene MO's

- 3D JMOL Molecular orbitals with synchronization