3
$\begingroup$

I want to output a molecular orbital diagram. Can anyone recommend a software to do this? Also I searched for a python module, but didn't found a pure solution. Maybe I am using the wrong keywords.

I want to connect two atoms with a specific electron configuration, to see at which energy levels they have pi- and sigma-bindings.

$\endgroup$
  • 1
    $\begingroup$ That depends, do you know what it's supposed to look like or are you asking about construction one where you don't know how it looks like? In the first case I've always been creative, for example using excel to draw the positions of the energy levels and then connect the rest by hand. If it's the latter case I fear you'd have to rely on computational chemistry first to determine the orbital energies. I'm using Orca to calculate that and Chemissian to draw the MO diagram afterwards. $\endgroup$ – Justanotherchemist Jun 25 at 11:17
  • 2
    $\begingroup$ I guess I still don't understand. Do you want to do a quantitative MO Diagram? Like one where you calculate the energy levels of the free fragments, then the energy levels of the corresponding MO, then use the linear combinations of the MO to draw the correlation lines? (Please don't use edit statements, simply extend your question. If anyone cares, every post has a history.) $\endgroup$ – Martin - マーチン Jun 25 at 11:57
  • 1
    $\begingroup$ I guess he's up to that. I'd say for a very simple view, so not taking the absolut energies for granted you could go with a quick calculation from any of the free softwares like Orca. And then use something like Avogadro to visualize the orbitals, check which ones are atom centered and which ones are molecular ones and take their energies. $\endgroup$ – Justanotherchemist Jun 25 at 12:02
  • 3
    $\begingroup$ Note, we have also a Matter Modelling site. $\endgroup$ – peterh - Reinstate Monica Jun 25 at 13:19
  • 1
    $\begingroup$ @Seminom I'd encourage you to edit that into your question in a way which you like; right now people are reading your question and thinking that it's not specific enough. Clarification in comments is good, but comments are temporary, so clarification in the question itself is even better. $\endgroup$ – orthocresol Jun 25 at 16:51
7
$\begingroup$
  • If your interest is a qualitative reprepresentation, you may reach out for an editor like inkscape and use lines, squares and Unicode to create a picture like the following one

    enter image description here
    In text fields you may enter Ctrl + U followed by an unicode code like 2191 (for $\uparrow$), 2193 (for $\downarrow$), 21C5 (for $\uparrow\downarrow$).*)
    If you have access to LaTeX, you may be interested in modiagram, especially if you are interested in an output as .[e]ps or .pdf. Only a few parameters are needed for an illustration like
    enter image description here

    (credit)

    (It is possible to construct more advanced orbital diagrams like this and this, too.)

  • For the quantitative, and more programmatic approach you seek, especially with Python, there are solutions with the matplotlib library which might require some adaptation by you (example). One of them is PyEnergyDiagrams once shown here on ChemSE: enter image description here

    the other EnergyLeveller.py: enter image description here

Addition: With the special chars used here, maybe a couple like Ipe + LaTeX is more handy to use, than inkscape.

| improve this answer | |
$\endgroup$
  • $\begingroup$ +1, and thank you for the open-source solutions, and especially for not suggesting to use ChemDraw for drawing MOs. $\endgroup$ – andselisk Jun 25 at 13:05
  • $\begingroup$ Thank you! That looks great. Do I have to calculate the levels before plotting or is PyEnergyDiagrams / EnergyLeveller able to calculate this just with information about the elements and their electron configuration? $\endgroup$ – Seminom Jun 25 at 14:19
  • 1
    $\begingroup$ @andselisk Beside open-source solutions, given the profile description by @Seminom, tools more likely accessible to a physicist than to a chemist appeared the better choice. The idea with ChemDraw did not occur to me, as the arrows / harpoons are available elsewhere with less effort, too. After all, the aim wasn't to check Powerpoint for Turing-completeness (short version: youtube.com/watch?v=uNjxe8ShM-8, long version: youtube.com/watch?v=_3loq22TxSc). $\endgroup$ – Buttonwood Jun 25 at 16:28
  • 1
    $\begingroup$ @Seminom No, each of the program expects you to provide the electron levels and splits. This is something quantum chemical programs like the free NWChem (nwchem-sw.org/index.php/Main_Page), Psi4 (psicode.org); or the commercial Gaussian may compute, and to some degree other physicist are capable to record experimentally. $\endgroup$ – Buttonwood Jun 25 at 16:41
  • 1
    $\begingroup$ @andselisk The longer video shows some of the hidden features not presented in the shorter one. As I recall, even using the transition of one irregular polygon into an other. On the other hand Tom Wildenhain went further, checks about compiling C with Powerpoint (youtube.com/watch?v=LArkm4v5mWA, github.com/TomWildenhain/pptcc) or «just» computing fractals (youtube.com/watch?v=O8l_awjgoMI, github.com/TomWildenhain/PowerPoint-Fractals). $\endgroup$ – Buttonwood Jun 25 at 16:49

Not the answer you're looking for? Browse other questions tagged or ask your own question.