How to find all aliphatic isonitriles?

To find all aromatic isonitriles this works:








c.C[N+]#[C-]





How to find all aliphatic isonitriles?

Hi,





As far as I know there is no simple way to do that as it is not possible to specify aliphatic molecule.





The aromatic molecule can be specified easily: molecule that contains aromatic atom. But the aliphatic molecule need the following specification (which cannot be defined as SMARTS): all atom is aliphatic.





Andras

Hi





You can set query properties for the atoms. The aliphatic/Aromatic switch is suitable for you.





However you can't store these properties in SMILES.








An example (in mrv format):

Code:

<?xml version="1.0" ?> <cml> <MDocument>   <MChemicalStruct>     <molecule molID="m1">       <atomArray           atomID="a1 a2 a3 a4"           elementType="C C N C"           formalCharge="0 0 1 -1"           mrvQueryProps="a0 0 0 0"           x2="0.0 4.180000000000001 5.720000000000001 7.260000000000001"           y2="0.0 -6.286520235623079E-17 -6.286520235623079E-17 1.257304047124616E-16"           />       <bondArray>         <bond atomRefs2="a2 a3" order="1" />         <bond atomRefs2="a3 a4" order="3" />       </bondArray>     </molecule>   </MChemicalStruct> </MDocument> </cml>

See





http://www.chemaxon.com/jchem/doc/user/query_features.html#atprop





or





http://www.chemaxon.com/marvin/help/sketch/sketch-chem.html#atom-props














Bye,





Robert

Robert,





That will not work if I don't want any aromatic atoms in the molecule.





Andras,





Maybe I could write SMARTS 5 and 6 membered rings with all atoms n or c with a "NOT" (!) in front of that? I just tried that but my SMARTS writing skills were not suficient to write that. If I could place a fragment like that in the query that that would remove most of aromatic compunds, if not all.

Hi,





The problem is the following:





You can match atoms with different properties.





But what you really need is the opposite (do not match), which is -as far as I know- is not possible.





So you can do it two steps:

1. Match isonitriles.
2. Get the results (result1).
3. Match aromatic atom (a) in this set.
4. Get the results (result2).
5. Exclude result2 from result1.

It is probably worth to mention that you can list the nonhits in search. So the steps 3, 4, 5 can be done in one search step.








Andras