Discussion

Thank you, cheminformatikers!

The latest version of Jmol has that issue fixed. See https://sourceforge.net/projects/jmol/files/Jmol/ and my comment at http://olcc.ccce.divched.org/2017OLCCModule2P2TLO3

A version of Hack-a-Mol that should work with charges (let me know if it does not!) is at https://chemapps.stolaf.edu/jmol/jsmol/hackamol.htm

https://chemapps.stolaf.edu/jmol/jsmol/hackamol.htm is a fixed version of Hack-a-Mol. Thanks for pointing out this issue with zwitterions. I will summarize the problem and the fix.

The way this page works to get a 2D version of the 3D file is for Jmol to generate the SMILES string for a structure and to send that to CIR as an identifier in a request for the JME string:

https://cactus.nci.nih.gov/chemical/structure/%5BNH3+%5DCC(%5BO-%5D)=O/file?format=jme

8 7 N 0.537 1 H 0 0.69 H 0.227 1.54 H 0.847 0.463 C 1.4 1.5 C 2.27 1 O 3.14 1.5 O 2.27 0 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 6 7 1 6 8 2

This JME string contains all the necessary information JSME (on the left) needs to display the model in 2D.

The problem is that CIR returns a JME string that is missing the charges. It's a bug on their end. So, what to do?

My solution utilizes some of the most powerful capabilities of Jmol, with a few features I added just now to work with JME strings. In order to do this, I had to make some changes in Jmol using a bit of Java programming. So this is only available in Jmol 14.9.0, which I just released at https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.9/Jmol%2014.9.0

Here's the idea:

1) Create an internal 2D model of the JME string returned from CIR consisting of nodes and connections.

2) Generate the SMILES string for that 2D model, and make a 1:1 map of each atom of that SMILES string to an atom of the 2D model.

3) Use the same SMILES string to also map all the atoms in the displayed Jmol model.

4) Use the two mappings to identify which atoms in the JME string are missing their charges, and fix them.

That's pretty fancy, but the bottom line is that by correlating each atom in the displayed 3D model with a specific atom in the 2D JME string, we can patch the known formal charges in the 3D model into the JME string at the right places. Here I am using a very special capability of Jmol: the ability to make a 1:1 correlation between the atoms listed in a SMILES string and the atoms of a model.

By doing this twice using the same SMILES string -- once with the 2D model derived from the JME string, and once with the 3D model -- we can correlate the atoms in the JME string to atoms in the 3D model.

Ah, that's interesting! The problem with the JSME app (2D, on the left) not recognizing the negative charge appears to be due to the fact that when Jmol request the JME format from CIR, which it needs to send to JSME, the call is this:

https://cactus.nci.nih.gov/chemical/structure/%5BNH3+1%5DCC(=O)%5BO-1%5D/file?format=jme

and the return is this:

8 7 N 0.537 1 H 0 0.69 H 0.227 1.54 H 0.847 0.463 C 1.4 1.5 C 2.27 1 O 2.27 0 O 3.14 1.5 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 6 7 2 6 8 1

Eh? you say?

8 atoms
7 bonds
[2D coordinates follow]
N 0.537 1
H 0 0.69
H 0.227 1.54
H 0.847 0.463
C 1.4 1.5
C 2.27 1
O 2.27 0
O 3.14 1.5
[Bonds follow, referencing atoms above]
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
6 7 2
6 8 1

But, wait -- no mention of charge!? The N has three Hs attached, so that can be figured out. But I'm afraid we are out of luck for the oxygen. JSME apparently doesn't know that we have specified ALL the H atoms, and it just supplies the missing on.

It's a limitation.

I will check with the author of JSME (Bruno Bienfeit) and see what he has to say; maybe I am just missing some sort of flag that will set this right....

....OK, what I have learned is that NCI has a bug in that it is returning an incorrect JME string when formal charges are present. The proper return would be something like this:

7 6 N+ 11.31 -5.97 C 9.86 -5.13 C 8.40 -5.97 O- 6.96 -5.13 O 8.40 -7.64 H 12.20 -5.45 H 11.31 -7.00 1 2 1 2 3 1 3 4 1 3 5 2 1 6 1 1 7 1

(Note the "+" and "-" signs there.)

Alas, that is the only server I know of that can do this, so I think we are out of luck on fixing that. It's a limitation.

Bob Hanson

Hi Dr Belford,

This is the file with the zwitterion and the text file showing radical. Thanks

C2H4NO2
APtclcactv02151711293D 0 0.00000 0.00000

9 8 0 0 0 0 0 0 0 0999 V2000
-1.8800 0.1413 -0.0000 N 0 4 0 0 0 0 0 0 0 0 0 0
-0.7085 -0.7954 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5711 0.0006 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5310 1.2192 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.6465 -0.5739 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-0.7456 -1.4236 0.8900 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7456 -1.4236 -0.8900 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.7392 0.8282 -0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5670 -0.7178 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
3 5 1 0 0 0 0
2 6 1 0 0 0 0
2 7 1 0 0 0 0
1 8 1 0 0 0 0
1 9 1 0 0 0 0
M CHG 2 1 1 5 -1
M RAD 1 1 2
M END
$$$$