Posted: Sat Dec 13, 2008 8:59 pmPost subject: Lewis formulas for Diazomethane

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.

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 ChemAxon personnel
Joined: 29 May 2005
Posts: 317

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.

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.

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 ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1163

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.

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.

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