Discussion

olcc s16 | Mon, 02/20/2017 - 14:16

In question 2 that we have to look up information in ChemSpider, I was doing search and ChemSpider only provides 1 SMILES string for each compound. In the assignment, there are canonical and isomeric. So, do we have to identify if that string is isomeric or canonical? I'm a bit confused.

Thanks
Phuc

Olcc S15 | Mon, 02/20/2017 - 13:30

Hello,
I was trying to find out if Omeprazole and Esomeprazole have the same Isomeric SMILES? Thanks

OLCC S104 | Mon, 02/20/2017 - 07:30

Hello there. I´m Damián Monllor, an Assistant Professor of Chemistry in IQS (Barcelona, Spain). I joined the course to avoid the "mind the gap" signal I always have in my head when computers and chemistry come together... I wish I can erase this sentence from my forehead once and for all (too optimistic, maybe). Best regards

Bob Hanson's picture
Bob Hanson | Sat, 02/18/2017 - 11:40

The reason this is happening is that hackamol.htm uses

var inchikey = Jmol.evaluateVar(jmol, "show('chemical inchikey')").trim();

instead of

var inchikey = Jmol.evaluateVar(jmol, "show('chemical stdinchikey')").trim();

I've corrected that at https://chemapps.stolaf.edu/jmol/jsmol/hackamol.htm and sent a note to admin to get it changed on this site as well.

Bob Hanson's picture
Bob Hanson | Sat, 02/18/2017 - 11:40

see above for my reply -- sorry, pressed the wrong reply button.

Bob Hanson's picture
Bob Hanson | Sat, 02/18/2017 - 11:39

Hello, S199 (Sorry, that's all I have for your name!)

Just wanted to say thanks for such great observation! Hack-A-Mol and Jmol are both better as a result. This is exactly what it's about in open-source software. Wonderful!

Bob Hanson - St. Olaf College

Sunghwan Kim | Fri, 02/17/2017 - 15:37

Let me explain why you got the unexpected results. Please follow the directions below to get the InChI and InChI strings directly from the NCI Resolver.

1. First use the NCI resolver to get the standard and non-standard InChI's for both neutral and zwitter ionic glycines through these links:

(1a) Standard InChI

Neutral: https://cactus.nci.nih.gov/chemical/structure/NCC(O)=O/stdinchi
Zwitter: https://cactus.nci.nih.gov/chemical/structure/%5BNH3+1%5DCC(=O)%5BO-1%5D/stdinchi

(1b) Non-standard InChI

Neutral: https://cactus.nci.nih.gov/chemical/structure/NCC(O)=O/inchi
Zwitter: https://cactus.nci.nih.gov/chemical/structure/%5BNH3+1%5DCC(=O)%5BO-1%5D/inchi

*** These are what you will get from the links above

(2a) Standard InChi

Neutral: InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
Zwitter: InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)

(2b) Non-standard InChI

Neutral: InChI=1/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)/f/h4H
Zwitter: InChI=1/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)/f/h3H

*** So the Standard InChIs for the neutral and zwitter ionic glycines are identicial to each other, while the non-standard InChI's are different. (Please pay attention to the FixedH layer beginning with "/f").

2. Now use the NCI resolver to get the standard and non-standard InChIKeys through these links.

(1a) Standard InChIKey

Neutral: https://cactus.nci.nih.gov/chemical/structure/NCC(O)=O/stdinchikey
Zwitter: https://cactus.nci.nih.gov/chemical/structure/%5BNH3+1%5DCC(=O)%5BO-1%5D/stdinchikey

(1b) Non-standard InChIKey

Neutral: https://cactus.nci.nih.gov/chemical/structure/NCC(O)=O/inchikey
Zwitter: https://cactus.nci.nih.gov/chemical/structure/%5BNH3+1%5DCC(=O)%5BO-1%5D/inchikey

*** These are what you will get from the links above:

(2a) Standard InChiKey

Neutral: DHMQDGOQFOQNFH-UHFFFAOYSA-N
Zwitter: DHMQDGOQFOQNFH-UHFFFAOYSA-N

(2b) Non-standard InChIKey

Neutral: DHMQDGOQFOQNFH-JLSKMEETNA-N
Zwitter: DHMQDGOQFOQNFH-TULZNQERNA-N

*** The standard InChIKey is the same for both forms of glycine, while the two forms have different InChIKeys. it is what should be expected from the definition of the standard InChI and InChIKeys.

3. I think you got the InChIs and InChIKeys by pasting the mol files into Hack-a-Mol. Try again with one of the mol file you got. To see what happened when you hit the "Enter" key, please click the "info" link above the 3-D view window. This will show a log of what just happened. Just scroll down to the buttom of this info box and you will see the followng two lines at the end:

(If you used the mol file for the neutral form)

FileManager opening url https://cactus.nci.nih.gov/chemical/structure/NCC(O)=O/stdinchi
FileManager opening url https://cactus.nci.nih.gov/chemical/structure/NCC(O)=O/inchikey

(If you used the mol file for the zwitter form)

FileManager opening url https://cactus.nci.nih.gov/chemical/structure/%5BNH3+1%5DCC(=O)%5BO-1%5D/stdinchi
FileManager opening url https://cactus.nci.nih.gov/chemical/structure/%5BNH3+1%5DCC(=O)%5BO-1%5D/inchikey

Pay attention to the last words on these URL. For some reason, Hack-a-Mol requested "stdinchi" and "inchikey", meaning that it got the Standard InChIs and the non-standard InChIs. So, that is the reason why you got the same InChI strings for both glycines, but different InChIKey strings for them.

I think Professor Hanson can tell us more details about this.

Robert Belford's picture
Robert Belford | Fri, 02/17/2017 - 15:10

Yes, she pasted each mole file back into hack-a-mol, to see if the two mol files gave the same InChI, which they do. But they do not give the same InChI keys. I also checked with Bob's site, and it is the same.

Robert Belford's picture
Robert Belford | Fri, 02/17/2017 - 14:49

She pasted the mol files from the bottom of the page (Sooyah.txt). One was the neutral, one was the zwitterion. Our logic was that if two files were of the same molecule, but one was neutral and the other was a zwitterion, the InChI should be the same. Which it was, but the keys are different.