Searching for N-phenyl indoles

I just noticed that these substructure queries

OC(=O)c1ccc(Nc2ccccc2)cc1

N(C1=CC=CC=C1)C1=CC=CC=C1

Do not find N-phenylindoles.

I think that is because the nitrogen is specified as aliphatic. To allow it to match indoles where the nitrogen is aromatic the bond type to the nitrogen would need to include aromatic. e.g. OC(=O)c1ccc(-[#7]c2ccccc2)cc1

Tim

I did wonder that but this works

C1=CC=C(C=C1)N1C=CC2=C1C=CC=C2

I tried

OC(=O)c1ccc(-[#7]c2ccccc2)cc1 and it does not work.

I used N-phenylindole as the query and it returned the results as expected, I then deleted the C3 of the indole and used it as the query and it did not return any indoles.

Hi Chris,

 

The Kekulé form of rings is converted to aromatic form during the search process.

If you delete atoms from the Kekulé form of the aromatic ring, you will break aromaticity and it will therefore not find the aromatic rings. However, you can use explicit aromatic or query bond types (like any, single/aromatic, etc) as well. An alternative is to use vague bond search options on the advanced search options panel.

 

See more information about this topic in the documentation:

http://www.chemaxon.com/jchem/doc/user/query_standard.html

http://www.chemaxon.com/jchem/doc/user/query_searchoptions.html#vaguebond

 

Let us know if you have further questions.

 

Best regards,

Szabolcs

tdudgeon wrote:

I think that is because the nitrogen is specified as aliphatic. To allow it to match indoles where the nitrogen is aromatic the bond type to the nitrogen would need to include aromatic. e.g. OC(=O)c1ccc(-[#7]c2ccccc2)cc1 Tim

Just realised there was a typo in your SMARTS if you use OC(=O)c1ccc([#7]c2ccccc2)cc1 it does work as required.

Thanks

Chris

Well, not a typo really. It depends on eactly what bonds you want to be treated as "single or aromatic".

See the attached for the difference. One extra bond is trated as "single or aromatic" in the second structure (your one).

Tim