Discussion

Sunghwan Kim | Mon, 02/20/2017 - 23:11

All databases we mentioned in this course are autonomous and independent of each other. So, I can't say why one database choose to do what. For the purpose of homework, if you don't find canonical SMILES or isomeric SMILES from ChemSpider, then indicate it with "N/A" or "None".

OLCC S197 | Mon, 02/20/2017 - 22:36

why is that Chemspider did not record the canonical and isomeric smiles of both omeprazole and esomeprazole.if it did please tell me how to get it.

OLCC s12's picture
OLCC s12 | Mon, 02/20/2017 - 21:07

This may just be a simple typo or I am misreading it, but I think the binary example used in the beginning for the phone number is for 904-620-1138 instead of 904-620-1938.

Evan Hepler-Smith's picture
Evan Hepler-Smith | Mon, 02/20/2017 - 20:22

Hi Phuc,

For a general discussion of "canonical" representations pertinent to this point, take a look at
"FORMULATING CHEMICAL STRUCTURE DATA" in part 1 of this module: http://olcc.ccce.divched.org/2017OLCCModule2P1

Thanks,
Evan

Sunghwan Kim | Mon, 02/20/2017 - 20:05

Isotope and stereochemistry information of a molecule is not encoded into its canonical SMILE (but into its isomeric SMILES). Therefore, the canonical SMILES cannot tell you whether the chiral center of a molecule has the (R)- or (S)-configuration.

Olcc S11 | Mon, 02/20/2017 - 17:31

" What you get back from a search is determined by the “representation” part of the URL and includes all of those above and ‘sdf’ (otherwise known as MOL file), ‘formula’ and ‘image’. So, using the URL below:
http://cactus.nci.nih.gov/chemical/structure/arsinic acid/names
prints out the names of this compound that are in the CIR system – for humans to read. If you use a computer to access the site (i.e. via a scripting language like PHP) you can also request the data be sent to you as XML using."

Here's my question since I'm unable to make an annotation in hypothes.is as part of this assignment:
Are there any other representations that can be searched for which are not listed here? Also, what is an XML?

OLCC S17 | Mon, 02/20/2017 - 17:27

In module 2.3-chemical representations, why is it that Omeprazole and Esomeprazole have the same canonical SMILES? any help please??

Sunghwan Kim | Mon, 02/20/2017 - 15:07

Omeprazole is a racemic mixture of (R)- and (S)-form, and its chemical structure has an unspecified stereo center. Esomeprazole is the (S)-enantiomer of omeprazole. Below is the link to the isomeric SMILES of esomeprazole.

https://pubchem.ncbi.nlm.nih.gov/compound/9568614#section=Isomeric-SMILES

Remember that isomeric SMILES contains isotope/stereochemistry specifications of a molecule. The SMILES string of esomeprazole contains the "@" symbol to explicitly show the (S)-configuration. Then, how about omeprazole, whose stereocenter has no explicitly specified configuration (e.g., either R or S)? Because of the absence of explicit chiral configurations, omeprazole does not have additional information to encode in its "isomeric" SMILES. (That is, its canonical SMILES and isomeric SMILES are identical. Therefore, the compound summary page of omeprazole shows canonical smiles only). On the contrary, you have both SMILES for esomeprazole.

Sunghwan Kim | Mon, 02/20/2017 - 14:50

Sorry for the confusion. If there is no isomeric smiles or canonical smiles, then indicate it with "N/A".

To distinguish whether a SMILES string is isomeric or not, check whether that SMILES string has any information about the isotopes or stereochemistry of the molecule. (e.g., "@", "@@", "/", "\", ......). If it does have any isotopic/stereochemical information, it is an isomeric SMILES.

Robert Belford's picture
Robert Belford | Mon, 02/20/2017 - 14:35

Hi All,

Here is an interesting way to import the data to a table, and this is one of the one's in Dr. Chalk's assignment. Open up a Google sheet and paste the following into a cell
=importhtml("https://www.organicdivision.org/orig/organic_solvents.html","table",1)

now, that is dynamic and linked to the original source, and will change if it changes, but you can copy and "paste values" into another part of the google sheet, and it is static.

You can also download as Excel from Google. There will be an error in the function as Excel using a different function that importhtml, but the data values will be pasted as raw text, with columns and everything formatted.

I think the "1' means first table.

Cheers,
Bob