Hi, I want to draw a benzene with delocalized conjugated bond(NOT with double or single-bond form) using avogadro, and I want to calculate the HOMO-LUMO values using orca with avogadro input file. Is there any way that I can make a molecule with delocalized electrons in orca?
Thatâs exactly how quantum chemical programs like Orca work.
You might draw isolated single and double bonds for a benzene. But quantum chemistry programs just get a set of atoms and positions (and the total charge on the molecule).
Itâs chemists that like to see single and double bonds, so Avogadro âperceivesâ them from the output files from Orca (or whatever program you use).
If you measure all the bond lengths after optimizing the geometry in Orca, youâll see that all the CC bonds are the same length.
Does that help?
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Thank you for answering.
But I want to make a input file for orca with Avogadro first, and then I want to get a orca output file(including HOMO-LUMO etcâŚ) using that avogadro input file.
I am not sure if I follow here. Let me recap for a moment:
- You want to use Avogadro to make an input file for ORCA
- You donât want to use the alternating single and double bonds for⌠some reason
The way I am seeing this is that you are mistaking the alternating bonds for not being a truly aromatic system, when in reality Avogadro knows that it is aromatic, but canât display the sort of âbond-and-a-halfâ that you may be looking for. Recall that benzene is, in terms of resonance, just two structures that flip between each other, as Iâve shown below.
I am in agreement with Geoff, you should create the molecule using the alternating double and single bonds, optimize with the Av2 force fields, and then optimize again with ORCA.