I'm pretty sure the squares of the orbitals are perfectly cylindrical. Why
do you say they are not?
sin^2(theta) + cos^2(theta) = 1
On Fri, Nov 23, 2012 at 2:33 PM, Shore, Jay <[email protected]> wrote:
>
> 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]>
> Reply-To: "[email protected]" <
> [email protected]>
> Date: Friday, November 23, 2012 8:05 AM
> To: "[email protected]" <[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]> 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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>
--
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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SAP, cloud infrastructure, etc. Download 30-day Free Trial.
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