Errror reading charge in a .mol file

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jwk
Posts: 36
Joined: Sat Jun 20, 2020 3:37 am
Full Name: John Keller
Organization: University of Alaska Fairbanks
Subdiscipline: Chemistry

Errror reading charge in a .mol file

Post by jwk »

WebMO v. 22 (demo site) and v. 19 (local) insert +3 charge on S when importing a .mol file.
Try this .mol file, which was exported from WebMO in mol/sdf format:
----------------------

WebMO

3 2 0 0 1 V2000
0.0000 0.6833 0.0000 S 0 1 0 0 0 0 0 0 0 0 0 0
-0.5726 -0.6896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.7356 0.9075 0.0000 O 0 -1 0 0 0 0 0 0 0 0 0 0
1 2 2 0
1 3 1 0
M END
-----------------------
Of course this is easy to correct manually, but I would like to provide for beginning students a .mol file that has idealized geometry and reasonable formal charges - as a starting point for further calculations. Is there another way to do this in WebMO so we get the correct formal charges after importing?

schmidt
Posts: 55
Joined: Sat May 30, 2020 3:00 pm
Full Name: JR Schmidt
Organization: WebMO, LLC

Re: Errror reading charge in a .mol file

Post by schmidt »

I can't import the snippet above, but it looks like SO2. When I export SO2 from WebMO as a MOL and then import, I get no charges, as expected. Can you elaborate?

jwk
Posts: 36
Joined: Sat Jun 20, 2020 3:37 am
Full Name: John Keller
Organization: University of Alaska Fairbanks
Subdiscipline: Chemistry

Re: Errror reading charge in a .mol file

Post by jwk »

(1) Build SO2 with 1 db and 1 sb. Add charges by right-clicking S (+1) and one O (-1). Then File, Export Molecule as mol/sdf format, creating a "molecule.mol" file in the download folder.
(2) Now start over: File, New. File, Import Molecule as mol/sdf, Choose File, find the above molecule.mol file, click OK.
Now display charges on the resulting molecule, showing +3 on S.

Step (1) would be what an instructor would do, wishing to distribute correctly-built-including-charges .mol files to students. With the .mol file (or text thereof) publicly available.
Step (2) would be what the student would do in order to import said molecule with charges.

jwk
Posts: 36
Joined: Sat Jun 20, 2020 3:37 am
Full Name: John Keller
Organization: University of Alaska Fairbanks
Subdiscipline: Chemistry

Re: Errror reading charge in a .mol file

Post by jwk »

More:
After assigning charges, do Cleanup, Comprehensive-Idealized.
The .mol text in the above window was modified by the Forum program so that it cannot be imported. To test my assertion, one would therefore need to rebuild SO2 per the directions given. Note that crucially the .mol file does record the formal charge assigned to each atom in the 6th field.

jwk
Posts: 36
Joined: Sat Jun 20, 2020 3:37 am
Full Name: John Keller
Organization: University of Alaska Fairbanks
Subdiscipline: Chemistry

Re: Errror reading charge in a .mol file

Post by jwk »

See the following web page for the formatted SO2 .mol test:

https://chem4.cns.uaf.edu/webmo1/so2-formatted-mol.htm

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