I'm new to MO-visualization and I'm using the program Orca to generate visualizations of molecular orbitals of a system of interest. I've been able to produce some nice images in VMD but I'm not sure what they actually mean:

enter image description here

I've seen pictures like this before with blue/red blobs to represent molecular orbitals, but I don't know what (specifically) they are representing. My suspicion is blue=HOMO and red=LUMO, or blue = negative wavefunction and red = positive wavefunction, but I'd like to know if there is a universal standard.

For reference, this is the "Graphical Representations" panel in VMD for this system: enter image description here


The colours represent the signal/phase of the molecular orbital, i.e. positive or negative. Below is the HOMO (made with ChemCraft) of butadiene (PBE-D3BJ/def2-SVP with ORCA) as an example.


Figure 1: HOMO of butadiene (cutoff 0.03)

ChemCraft shows by default negative phase as blue and positive as red. VMD seems to follow the same convention.

You can certainly change the colours if you want. Below is how the controls for surfaces in ChemCraft look like:

Surface controls in ChemCraft

Figure 2: surface controls in ChemCraft

Other programs may use different conventions, such as NBOView (yellow and blue).

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    $\begingroup$ The advantage of yellow and blue or red is that if you print them monochrome, you can still make out the phases. This is a lot harder for red and blue. But I'm not aware of any convention that is predominant. Black and white is also a good choice, as it matches most schematics. I personally use different colour schemes for doubly occupied, singly occupied and unoccupied orbitals. $\endgroup$ – Martin - マーチン Mar 7 '17 at 21:21

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