Hi, I am a new Avogadro user who is doing summer research into 3d modeling for chemistry education. Is there any functionality out there that allows for visible displays of lone pairs? I have tried looking on the internet, however, most videos are typically a few years old.
Also, where is a good place to start learning how to better use Avogadro for someone with limiting coding experience?
You likely refer to the visualization of molecular orbitals as for example for ethene in the example below
for which Avogadro helps you to set up the necessary (start) data to perform the necessary (quantum chemical) computations in programs separate to Avogadro. In Avogadro, check if the click on
input opens a pull down menu similar like this one:
subsequently opening a mask like
If absent, install the Avogadro generators (
With the results of the computation (e.g. by Gaussian, MOPAC, etc) in hand in special files, you then have to select the orbital(s) of interest (similar as described to the tutorial here). Coding experience would be helpful/a requirement if you want to modify the Avogadro program. However for the construction of simple molecules, the setup of the computations sent to Gaussian, and a visualization of the results you do not need this additional background.
For smaller molecules (where computation of the molecular orbitals is faster / more affordable), chemcompute.org offers some relevant lab classes. I recommend to venture out the “How to perform quantum calculations” (in General Instructions), then “Basic atomic and molecular orbitals” (in General Chemistry) – both accessible in section GAMESS/Psi4 as one point of entry. In addition to this, get in touch with your hosting group, they likely can provide you with additional material specific to the program(s) they use / additional theoretical background for a sound start.