Numbering of structures drawn by chemspider

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  • Joined: 02/13/13

Numbering of structures drawn by chemspider

Posted by James Pash on Feb 13, 2013 1:49 pm

Is there a way to show the numbers of each carbon that is drawn in Chemspider? I need to check quickly if two compounds with different and somtiimes incorrect IUPAC names are really the same compound, The names don't always post in Chem Spider. I would be a great help to have this feature. 
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  • Joined: 07/30/09

Re: Numbering of structures drawn by chemspider

Posted by David Sharpe on Feb 15, 2013 7:01 pm

Hi James,

I'm afraid that what you are asking is not actually possible. There isn't a canonical/absolute way of numbering a chemical. That is to say, atom numbering is not a property of the molecule, it is an attribute of the nomeclature system and how it is applied. Take for example: http://www.chemspider.com/Chemical-Structure.13835772.html.
Here, the name 2-Methylphenol uses the position of the (phenolic) hydroxy group as the intial reference point (i.e. carbon 1) so the methyl group is in the 2-position. 

But in the name 2-hydroxytoluene, the numbering is based on the methyl group being the point of reference (i.e. carbon 1) and the hydroxy group is in the 2 position.

It is for this reason that in a ChemSpider record we make the chemical structure the basis for the record and then link data and names to that.

If you have any further questions relating to this or any other aspect of ChemSpider, please do get in touch again - either in these forums or by emailing the ChemSpider team directly (chemspider-at-rsc-dot-org).

Kind regards,

Dave
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  • Joined: 02/20/13

Re: Numbering of structures drawn by chemspider

Posted by Daniel Lowe on Feb 20, 2013 12:58 am

Hi James,

If two names describe the same structure you should end up at the same page on Chemspider. When you perform a search on Chemspider your name is checked against the known names for compounds in the database and as a fall back an attempt is made to convert the name to a structure algorithmically.
As name to structure conversion is a non trivial problem, if ChemSpider does not recognise the name other services like http://opsin.ch.cam.ac.uk/ or http://cactus.nci.nih.gov/chemical/structure may nonetheless to convert your name to a structure. To check identity of organic molecules between sites one can compare InChIs.

Depending on what you meant by the IUPAC names being incorrect there is a possibility that no service will be able to make sense of them!
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