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 Orbtials) 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 Orbtials will have a button underneath the viewer like so.

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 Jmol screen will give additional options and features that can be explored for the reaction.

Example 1 - A Simple Sn2

Background Colour:


Example 2 - [1,5] Hydrogen Shift

Background Colour:


Two 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


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