A number of programs are available that let you build, visualize, and analyze 3D models of chemical structures (I use Chem3D/ChemBio3D). Current versions usually include various possibilities for the calculation and graphical representation of molecular orbitals.

buta-1,3-diene HOMO

However, the resulting images can be overloaded or unclear. Introductory explanations using such images might be overdoing it. Therefore, many textbooks on organic chemistry use simple chemical structure diagrams based on atomic orbitals.

buta-1,3-diene HOMO

In particular for didactic purposes, I am looking for an intermediate solution. I would like to build, optimize, and visualize a 3D model of a chemical structure and show a graphical representation of the original atomic orbitals in the 3D model. Unfortunately, this option doesn’t seem to be available in Chem3D/ChemBio3D. Does any software exist that lets you build a 3D model of a chemical structure and visualize atomic orbitals?

  • $\begingroup$ I haven't come across something like that but I have been wanting something like it as well. I could imagine that it might be possible to achieve this with Avogadro if you are proficient enough with it and C++ to write some sort of plugin. $\endgroup$
    – Philipp
    Jul 5, 2016 at 16:40
  • $\begingroup$ >Does any software exist that lets you build a 3D model of a chemical structure and visualize atomic orbitals? || to my knowledge, no. However, QC packages often offer 'natural orbital analisys', that among other things prints participation of atomic orbitals in molecular orbitals. You can also visualize individual atomic orbitals in some cases and copy-paste them. $\endgroup$
    – permeakra
    Jul 5, 2016 at 17:12
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    $\begingroup$ I'm not entirely sure what you want. For example, you say "can be overloaded or unclear" and "might be overdoing it." In my experience, most students can grasp molecular orbitals (or the natural orbital transformations) well. You just need to pick rendering options (e.g., partial transparency) that suit your needs. $\endgroup$ Jul 6, 2016 at 3:20
  • $\begingroup$ To follow on the other comments, besides doing a natural orbital analysis (a good option - you can then use most software to view the results), I am not aware of any such software. However, there are probably ways to hack this even without coding a rendering option. If you want to pursue it, consider contacting me. $\endgroup$ Jul 6, 2016 at 3:21
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    $\begingroup$ The "overloading" likely arises from default parameters for the isosurface used to display. Just increase that and the MOs will look less crazy. $\endgroup$ Jul 7, 2016 at 15:01

1 Answer 1


As porphyrin mentions in the comments, have a look at Jmol.

enter image description here

It indeed does the rendering as in your original version, but with the many options (see this mo command documentation) and particularly interactivity provided by the scripting, I think you may pedagogically achieve what you are looking for. Proteopedia is a nice website where the efficiently use Jmol's scripting feature for educational purposes (try the green links).


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