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Identification of heteroaliphatic rings as basic / non-basic
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timritchie

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Link to postPosted: Mon Aug 09, 2010 9:10 amPost subject: Identification of heteroaliphatic rings as basic / non-basic Reply with quote

Hello,

Is it possible to calculate the number of heteroaliphatic rings in a set of molecules that are basic (e.g. contain a positively ionisable amine) and those that are non-basic (e.g. a cyclic amide or an ether).

Thanks,

Tim Ritchie.

Gyuri
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Link to postPosted: Tue Aug 10, 2010 7:25 amPost subject: Reply with quote

The question is complex, so the solution is too, but doable. You can first filter out the "set of molecules that are basic (e.g. contain a positively ionisable amine) and those that are non-basic (e.g. a cyclic amide or an ether)" using a combination of a query (probably formulated in SMARTS) and a Chemical Terms expression (containing a pKa calculation for example). Then you can use the heteroaliphaticRingCount function of TopologyAnalyser to get the number you want for each structure.

Depending on your preference, you can solve this issue in command line (jcsearch, see its -e swith for additional CT expression) or in a desktop application environment (Instant JChem) or even by developing your own little program on the basis of the the JChem API (Java, .NET or Web Services).

timritchie

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Link to postPosted: Wed Aug 11, 2010 9:35 amPost subject: Reply with quote

Thanks for that. Could you suggest a SMARTS query to identify basic amines that are cyclic rather than acyclic.

Regards,

Tim Ritchie.

Gyuri
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Link to postPosted: Wed Aug 11, 2010 9:58 amPost subject: Reply with quote

If you mean, that an amino group is connected to a carbon of a cycle, try his:

[CX4R][NX3;!$(NC~[!#1!#6])]

It means an aliphatic carbon with 4 neighbours (including hydrogens), member of a least a ring, connected a nitrogen wih 3 neighbours and that nitrogen is not connected to a carbon that is connected to a hetero atom

timritchie

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Link to postPosted: Wed Aug 11, 2010 10:22 amPost subject: Reply with quote

Sorry, I wanted the nitrogen atom to be in the ring, secondary or tertiary, and not part of an amide.

Gyuri
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Link to postPosted: Wed Aug 11, 2010 10:32 amPost subject: Reply with quote

The one I showed is not part of an amide, I am sure, that you can easily move the ring property (R) from the carbon to the nitrogen. I would suggest to take a look a the SMARTS tutorial and examples, it will help you to refine this initial SMARTS further as you wish and design make others in the future.

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