Organic Chemistry Animations

Introduction to Animated Molecular Orbitals

Animated Molecular Orbitals are a new way to view Chemical Reactions.

Each reaction shows how important orbitals (Intrinsic Bonding Orbitals) change during a reaction.1

These animations can be used to help understand curly arrow mechanisms.

Use the examples below to understand how these animations work and how they can help to understand reactions in more depth.

Pages with these Animated Molecular Orbitals will have a button underneath the viewer. Please be patient, they may take a few seconds to load.

Use the "Larger View" button to open a new window where you can control the animation.

Use your scroll wheel to enlarge and shrink the models, right clicking the mouse (Control-click MacOS) over the resizeable JSmol screen will give additional options and features that can be explored.

Example 1 - A Simple SN2

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Example 2 - [1,5] Hydrogen Shift

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Two gallery pages have been created highlighting all the Animated Molecular Orbital Reactions created for ChemTube3D.

Introductory Organic reactions | Pericyclic Reactions and Heck Catalytic Cycle

These animations have been made possible by the programme IboView with the assistance of the authors and the addition of specific features to JSmol by Bob Hanson.


1. G. Knizia and J. E. M. N. Klein, Angew. Chem. Int. Ed. Engl., 2015, 54, 5518–22 and G. Knizia, J. Chem. Theory Comput., 2013, 9, 4834–4843.