filtering molecules containing non-organic elements

Hi all,

I'd like to know how to filter molecules containing non-organic elements (e.g. OE = H, C, N, O, F, Si, P, S, Cl, Br, and I...as defined in pubchem) using Jchem4Excel or any ChemAxon tool.

Thank you,

Oscar

Hi Oscar,

Structure Checker has a Rare Element Checker. It detects if a structure contains elements that are not usual in organic compunds. However, it takes into account a different set of elements than you mentioned. It considers the following atoms to be generally occuring:  H, Li, Na, K, Mg, Ca, B, C, N, O, F, Cl, Br, I, Al, P, S, Cr, Mn, Fe, Co, Ni, Cu, Zn. Unfortunately this list cannot be manipulated by the users.

To use it in Excel you need the JCCheck if just want to get a simple true or false answer. Use the actionstring "rareelement".

http://www.chemaxon.com/jchem4excel/userguide/structure_checker.html

http://www.chemaxon.com/marvin/help/structurechecker/checkerlist.html#rareelement

I hope it helps you!

Regards

Attila

Dear Attilas,

Thanks for your kind and useful response. It'd be great if you could enable this tool also for users in a near future.

Cheers,

Oscar

Hi Oscar,

 

this issue has popped into my mind recently and I have found a solution for this, however, it is not that convenient.

Structure Checker has a Substructure Checker but unfortunately it is not available in Excel yet. You can still find it in our Structure Checker application. A SMARTS string need to be defined to do substructure searches. In your case this should look like this:

[!#1!#6!#7!#8!#9!#14!#15!#16!#17!#35!#53]

It warns you if a structure contains an element other than H, C, N, O, F, Si, P, S, Cl, Br,  I.

Looks ugly because the elemnts are defined by their atomic number because SMARTS makes difference between lower and uppercase letters whether they aromatic or not, so the string can be shorter in this way.

 

I hope it helps you!

Cheers

Attila