This brings up a very interesting point – the electron density is not just the
sum of the squares of the orbitals. Think about carbon monoxide – the electron
density is perfectly cylindrical while the square of the orbitals is not.
From: Robert Hanson <[email protected]<mailto:[email protected]>>
Reply-To:
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Date: Friday, November 23, 2012 8:05 AM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [Jmol-users] Molecular Orbitals squaring
This is great! Your idea will be used by many, I am sure. Organic chemists like
to talk about electron density, and we often calculate it from charge density,
but this sets the stage for doing this from MOs. For now, it's just specific
sets of orbitals, but I can make that work for all occupied orbitals based on
occupancy. Very nice!
OK, I'll check out the Molden file reading. Jmol reads MOs up through F.
Bob
On Thu, Nov 22, 2012 at 6:02 PM, Leonardo Matheus
<[email protected]<mailto:[email protected]>> wrote:
Dear Bob,
Thank you very very much! That is exactly what I wanted, and indeed the benzene
example is great!
But unfortunately I had two problems, for which I have posted examples at my
webpage at http://romeo.if.usp.br/~leommj (I'm new here at the mailing list,
and don't know if I could send attachments instead).
1) For long molecules, the squared orbitals are cut in the middle of the
molecule. As this happens with different orbital combinations, and the
(non-squared) MOs extend through all the molecule, I think this should be a
bug. An example for this bug is on the file OC8H10.molden at the website above.
2) I can't plot the orbital of thiophene (squared or not). Does Jmol have a
problem with d orbitals (I hope not, as I intended to use molecules with other
third row elemets)? Or is it just a compatibility problem with my .molden
files? This file is named SC4H4.molden at the same webpage.
PS: I already had one such compatibility problem between my files and Jmol; I
had to manually add a space between "[Atoms]" and "(Angs)" on the second line
of the file for Jmol be able to read them.
Many, many thanks for your help!
Leonardo Jorge
PhD Student at USP - Brazil
Nanomol group
http://nanomol.if.usp.br
------------------------------------------------------------------------------
At Thu, 22 Nov 2012 10:40:14, Robert Hanson wrote:
Leonardo,
___JmolVersion="13.1.9_dev"
new feature: MO [0.5 21 0.5 20] SQUARED
-- squares MO psi functions as it combines them.
see http://chemapps.stolaf.edu/jmol/Jmol-13.zip
Let me know if that is what you were talking about. I think it is.
VERY interesting result with
load c6h6.smol
mo [0.5 20 0.5 21] squared
This is the degenerate pair of HOMO orbitals. The result is a symmetric
electron density equivalent at each carbon.
Bob
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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