# Resonance formulas are not isomers

User 25d107bd42

07-12-2008 22:12:19

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

User 25d107bd42

07-12-2008 22:17:27

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

User 851ac690a0

08-12-2008 10:40:23

Hi,

Yes, I agree

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

Jozsi

User 25d107bd42

08-12-2008 11:03:06

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

ChemAxon 5433b8e56b

09-12-2008 13:09:18

Dear Hans-Urlich!

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

Best regards,

Istvan

User 25d107bd42

13-12-2008 10:51:42

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

User 25d107bd42

13-12-2008 19:59:59

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.

User 25d107bd42

13-12-2008 20:04:50

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.

User 25d107bd42

13-12-2008 20:08:46

Results for the Lewis formula LF2 as "input".

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

User 25d107bd42

13-12-2008 20:14:48

Results for the Lewis formula LF3 as "input".

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

User 25d107bd42

13-12-2008 20:19:19

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

User 25d107bd42

14-12-2008 08:52:22

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

ChemAxon e08c317633

17-12-2008 16:30:39

**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
ChemAxon 8b644e6bf4

18-12-2008 02:52:57

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

User 25d107bd42

18-12-2008 08:35:16

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

User 25d107bd42

18-12-2008 08:44:16

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

ChemAxon e08c317633

23-12-2008 00:44:27

**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
User 25d107bd42

23-12-2008 08:05:20

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