Multi Attachment questions

I am trying to replicate the following markush statements electronically:

1) R9 is a 5 to 7-membered unsaturated heterocyclic ring which is optionally substituted by one or more substituents R15

I can explicitly draw out each het accounting for each possible markush attachment point (see Exp_1.mrv), but when I try to generalize the markush attachment point by attaching it to the multi center attachement point, I get an error. Is there a more elegant way to accomplish what I have shown? Also, is is possible to encode for 1 to N R15 groups with varriable attachement points?

2) R1 is a C1-5 alkyl group optionally substituted by one or more R10 groups

I have found a solution (Ex_2.mrv) where R10 can also be H that catches C2-5 (C1 is done as a separate entry), but I wonder if there is a better solution. I found a previous forum post that that uses repeating groups and variable attachements (problems.mrv), but when I try to ennumerate the structures, I get an error (it works fine when the multi center attachement is removed).

Thanks in advance

Robert

Hi Robert,

 

The erroneous structure can be corrected if the position variation bond and it's endpoint are both included in the repeating unit. 

The other markush structures I would represent with homology groups. Your two stuctural groups alkyl and heterocycle are both included in the list ofsupported  homology groups. 

http://www.chemaxon.com/marvin/help/calculations/homologygroups.html#definition

You can also add properties with which you can refine the represented structures. 

Description of possible properties: http://www.chemaxon.com/marvin/help/calculations/homologygroups.html#homology_properties

Editing properties and drawing markush:

http://www.chemaxon.com/marvin/help/sketch/sketch-basic.html#markush-structures

Multiple occurences of the same attaching R15 should be drawn separatelly it's not supported currently. 

You can attach the several occurrences of the given Ratom to the same homology atom and allow hydrogen as a definition for this R atom.  This may be incorrect if such a structure does neither have enough hydrogens to cover the explicit hydrogens of the definitions nor the required heavy substituents.

Homology groups are not fully enumerated they are only enumerated based on a set of definitions, but any structure that fullfils the needed requirements can match such a group. (and can be matched by the group if the group is on the query side.)

I attach solutions for your problems.  

Robert

Thank you very much, that was very helpful. Your examples have helped me get a better handle on homology groups. 

Looking back at my initial question, I just realized I got my self turned around on the language used in the Markush claim relating to the unsaturated heterocyclic ring. Consequently, I drew all my unsaturated heterocyclic rings as saturated hetrocyclic rings. Silly mistake on my part. Sorry for any confusion and thank you for answering the question I actually meant to ask. 

Could I ask for a bit clarification on this statement:

You can attach the several occurrences of the given Ratom to the same homology atom and allow hydrogen as a definition for this R atom.  This may be incorrect if such a structure does neither have enough hydrogens to cover the explicit hydrogens of the definitions nor the required heavy substituents.

Could you provide an example of what you mean?

Thank you

Robert

rwagner wrote:

Hi Robert,   The erroneous structure can be corrected if the position variation bond and it's endpoint are both included in the repeating unit.  The other markush structures I would represent with homology groups. Your two stuctural groups alkyl and heterocycle are both included in the list ofsupported  homology groups.  http://www.chemaxon.com/marvin/help/calculations/homologygroups.html#definition You can also add properties with which you can refine the represented structures.  Description of possible properties: http://www.chemaxon.com/marvin/help/calculations/homologygroups.html#homology_properties Editing properties and drawing markush: http://www.chemaxon.com/marvin/help/sketch/sketch-basic.html#markush-structures Multiple occurences of the same attaching R15 should be drawn separatelly it's not supported currently.  You can attach the several occurrences of the given Ratom to the same homology atom and allow hydrogen as a definition for this R atom.  This may be incorrect if such a structure does neither have enough hydrogens to cover the explicit hydrogens of the definitions nor the required heavy substituents. Homology groups are not fully enumerated they are only enumerated based on a set of definitions, but any structure that fullfils the needed requirements can match such a group. (and can be matched by the group if the group is on the query side.) I attach solutions for your problems.   Robert

 

Hi Robert,

Well my assumption about this problem was bad, such structures exist but they are retrieved by the search.

The attached query and target shows a case where the query ring can't have as much implicit H/explicit H/heavy atom neighbours as required in the target. 

This is not a problem in case of substructure search, because the query is contained in the target.

In full search not all the target Rgroups are covered by the query, this would prevent match for Rgroups with only heavy atom definition, but if an Rgroup has a single hydrogen definition as well, it's not required in a full match. 

Hence the solution where the maximal number of Rgroups are attached to the ring and the Rgroups have a hydrogen definition is suitable for your purpose. 

Regards,

Robert