SMARTS definition

I want to represent H or any C but not connected to aliphatic carbonyl group. Is this representation correct. What could be better and most accurate. [#1,#6;!$(C=[O])]

the use of this term will be in lets say, representing enol derivatives as:

[C;!$(C[OH,SH]):1]=[C:2][OX2,SX2:3][#1,#6;!$(C=[O]):4]

Hi Barun,

Yes, your SMARTS expression looks correct.

You may also try it on one of the public tryout pages, and see the results yourself:

 

http://www.chemaxon.com/jchem/examples/sss/index.jsp

http://www.chemaxon.com/ajax/

 

or you may use the jcsearch command line tool to check matching atoms:

$ jcsearch --allHits -q '[#1,#6;!$(C=[O])]' 'CCC(O)(C(C)=O)C(O)=O'
    Query has 9 matches:
        Match 1:[    1 ]
        Match 2:[    2 ]
        Match 3:[    3 ]
        Match 4:[    6 ]
        Match 5:[   -1 ]
        Match 6:[   -2 ]
        Match 7:[   -4 ]
        Match 8:[   -6 ]
        Match 9:[   -9 ]
CCC(O)(C(C)=O)C(O)=O

 

Best regards,

Szabolcs

Hi,

The first atom in the recursive expreession is the atom to which it is given. So searching for hydrogens and carbon not attached to an C=O  can be done by:

[#1,#6;!$([A,a]C=O)]

Instead of [A,a], [#1,#6] can be written as well.

Note that such a query will match the carbon in the carbonyl group if it is not attached to an other carbonyl group.

Bye,

Robert

Szabolcs, thanks for the link, the first one i am aware of.

rwagner, so does that mean any H (individual H and not the one attached to C=O) and carbon attached to C=O?

what you mean is like this? [#1,#6;!$([#6]C=O)]

Or the SMARTS expression for enol derivative will give me an enol also? which ends with - OX2H

Thanks.

Hi,

The original expression you've written accepts any hydrogen and carbon except carbons having double bonded oxigen.

The expression [#1,#6;!$([#6]C=O)] will accept any hydrogen and carbons expect carbons attached to a C=O. I wrote [A,a] or [#1,#6] instead of [#6] to exclude hydrogens attached to a C=O as well.

Bye,

Robert

Thanks for the earlier reply. I have one more Question.

I am not clear on these two forms of representation for Hydrogen: [H] (explicit Hydrogen?) or [#1]

Could you please highlight the difference and why they give different results when queried. Probably my concept of Explicit hydrogen is not clear.

Hello,

 

[H] and [#1] mean the same both mean hydrogen atoms. However in SMARTS H<n> after an atom symbol means number of hydrogens on the given atom.

see http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html

Which searches did give you different hits?

Bye,

Robert