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Resonance formulas are not isomers
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Hans-Ulrich

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Link to postPosted: Sun Dec 07, 2008 11:12 pmPost subject: Resonance formulas are not isomers Reply with quote

Hi, there are more problems about resonance formulas.

On the right hand side of MarvinSketch there is the Tool "Isomers - Resonance", see the screenshot.

Resonance formulas are VB wave functions and not isomers.

Having already mentioned this wrong nomenclature in other topics, I have really problems to use Marvin for teaching.

I must also attach once more the IUPAC comment.

In the following post I will show my suggestion to solve these problems.

Regards, Hans-Ulrich
Hans-Ulrich

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Link to postPosted: Sun Dec 07, 2008 11:17 pmPost subject: Reply with quote

Here is my suggestion to make a separate new line for the Tool - Resonance.

It must be clearly separated from "isomers".

It's important to have clear exact nomenclature.

Regards, Hans-Ulrich
Jozsef
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Link to postPosted: Mon Dec 08, 2008 11:40 amPost subject: Reply with quote

Hi,


Yes, I agree
Instead of the Tool's name "Resonance" I just simple will call this Tool as "Lewis-structures".


Jozsi
Hans-Ulrich

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Link to postPosted: Mon Dec 08, 2008 12:03 pmPost subject: Reply with quote

Hi,

that's a really good information.

Generate a new tool and call it "Lewis-structures".

This would avoid the rather dubious word "resonance".
This word is responsible for many misunderstandings.

I have a further comment about "canonical", but on this topic I'm awaiting the comment of a colleague.

Hans-Ulrich
István
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Link to postPosted: Tue Dec 09, 2008 2:09 pmPost subject: Reply with quote

Dear Hans-Urlich!

We will inform you in this topic, when the modification of the menu is released.

Best regards,
Istvan
Hans-Ulrich

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Link to postPosted: Sat Dec 13, 2008 11:51 amPost subject: Reply with quote

Hi,

I have one additional suggestion: Call it Lewis formulas.

This would avoid misunderstanding these formulas as real things.
The Lewis formulas are only contributions to the valence bond wavefunction.

Regards, Hans-Ulrich
Hans-Ulrich

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Link to postPosted: Sat Dec 13, 2008 8:59 pmPost subject: Lewis formulas for Diazomethane Reply with quote

Hi,
further evaluating the tool handling resonance formulas = Lewis formulas I will first attach the corresponding Help-manual. Here the example is diazomethane.

As you see in the next three posts, I got different results. Especially the so called "canonical form" is different.
Hans-Ulrich

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Link to postPosted: Sat Dec 13, 2008 9:04 pmPost subject: Reply with quote

Results for the Lewis formula LF1 as "input".

"Take major contributors" give three the Lewis formulas LF1, LF2 and LF3.
One more than in the help manual.


Last edited by Hans-Ulrich on Sat Dec 13, 2008 9:20 pm; edited 1 time in total
Hans-Ulrich

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Link to postPosted: Sat Dec 13, 2008 9:08 pmPost subject: Reply with quote

Results for the Lewis formula LF2 as "input".

"Take major contributors" give two Lewis formulas LF1 and LF2.
Hans-Ulrich

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Link to postPosted: Sat Dec 13, 2008 9:14 pmPost subject: Reply with quote

Results for the Lewis formula LF3 as "input".

"Take major contributors" give two Lewis formulas LF1 and LF3.
Hans-Ulrich

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Link to postPosted: Sat Dec 13, 2008 9:19 pmPost subject: Reply with quote

To summarise the results of these tests:

Starting with different Lewis formulas for the same molecule give different results,
but the results must be the same.

Regards, Hans-Ulrich
Hans-Ulrich

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Link to postPosted: Sun Dec 14, 2008 9:52 amPost subject: Reply with quote

Hi,

a further test shows different results for the conformer-energy calculation for the three Lewis formulas of diazomethane, see screenshot.

BTW: The carbenium substructure is normally planar, in LF3 it's pyramidal.

Regards, Hans-Ulrich
Zsolt
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Link to postPosted: Wed Dec 17, 2008 5:30 pmPost subject: Reply with quote

ifajth wrote:
We will inform you in this topic, when the modification of the menu is released.
Hi Hans-Ulrich,

In Marvin 5.2 "Resonance" plugin will be moved from the "Isomers" group to the "Other" group, and it will be free (will run without license key). I hope this is a suitable solution for you.

Zsolt
Gabor
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Link to postPosted: Thu Dec 18, 2008 3:52 amPost subject: Reply with quote

Dear Hans-Ulrich,

Lewis formulas are usually recognized as different structures in MM calculations. This is the case in Clean3D/Dreiding where only atomic numbers and bond orders are considered only; consequently one can not compare energies of these "different" structures.

As far as i know a few such equivalences are coded into MMFF94, so when we introduce its implementation in the future it will solve some of these problems.

Additionally let me notice that the proper 3D handling of these structures possibly calls for more sophisticated methods, such as quantum chemistry calculations.

Regards,
Gabor
Hans-Ulrich

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Link to postPosted: Thu Dec 18, 2008 9:35 amPost subject: Reply with quote

Hi Zsolt, now I have once more two topics in one.

Let me first answer to your post about the option "resonance". No, I don't find this suitable.
Why is there the "Other" option at all. Why is Huckel Analysis "Other" and Markush Enumeration not ? This is not consequent.

I suggest to eliminate the option "Other" and to put all the options in one long menu list, as shown in the attached picture.

MarvinSketch has many different "Calculations" integrated other programs don't have.
So it would be a good presentation to show these "Calculations" possibilties in a large list.

I further suggest to call these implemented programs: "Calculations". These valuable programs are more than simple tools.

A good GUI has to be as intuitive as possible.

Regards, Hans-Ulrich
Hans-Ulrich

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Link to postPosted: Thu Dec 18, 2008 9:44 amPost subject: Reply with quote

Dear Gabor,

I must change my answer.The sentence "Lewis formulas are usually recognized as different structures in MM calculations."
shows really the problem of Dreiding MM calculations.

In the parameter table I of Goddard's paper (J.Phys.Chem. 1990, 94, 8897-8909) there are f.e. different parameters for single, double and other CC-bonds.

So it's a real problem how to manage Lewis formulas.

Regards, Hans-Ulrich
Zsolt
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Link to postPosted: Tue Dec 23, 2008 1:44 amPost subject: Reply with quote

HUWagner wrote:
Hi Zsolt, now I have once more two topics in one.

Let me first answer to your post about the option "resonance". No, I don't find this suitable.
Why is there the "Other" option at all. Why is Huckel Analysis "Other" and Markush Enumeration not ? This is not consequent.

I suggest to eliminate the option "Other" and to put all the options in one long menu list, as shown in the attached picture.

MarvinSketch has many different "Calculations" integrated other programs don't have.
So it would be a good presentation to show these "Calculations" possibilties in a large list.

I further suggest to call these implemented programs: "Calculations". These valuable programs are more than simple tools.

A good GUI has to be as intuitive as possible.

Regards, Hans-Ulrich
Thanks for your comments.
The menu is customizable. Here you can find the description about "Tools" menu customization: http://www.chemaxon.com/marvin/help/developer/plugins.html#config

I hope this helps,
Zsolt
Hans-Ulrich

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Link to postPosted: Tue Dec 23, 2008 9:05 amPost subject: Reply with quote

Hi Zsolt,

No, that does not help.

To have the possibility to customize my own help menu doesn't solve the general problem.
The general problem is, there is a fine applet in the web to handle chemical formulas and to manipulate molecules and ions,
but this applet and the distributed MarvinSketch use bad and wrong denotations for the menus and the tools.

So it's difficult to use it for teaching chemistry.
Teaching chemistry is not easy. So at least the denotations and definitions must be accurate.

I hope you will implement the revisions in your next releases.

Regards, Hans-Ulrich
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