Keying elements, functional groups

Structural keys describe the chemical composition and structural motifs of molecules represented as a Boolean array. If a certain structural feature is present in a molecule or a substructure, a particular bit is set to 1 (true), otherwise to 0 (false). A bit in this array may encode a particular functional group (such as a carboxylic acid or an amidelinkage), a structural element (e.g., a substituted cyclohexane), or at least n occurrences of a particular element (e.g., a carbon atom). Alternatively, the structural key can be defined as an array of integers where the elements of this array contain the frequency of a specific feature in the molecule. 

Additional keying information can come from certain other structural features which are present in a retron- or partial-retron-containing substructure. These ancillary keying elements can consist of functional groups, stereocenters, rings or appendages. Consider target structure 5... 

The second element of general importance in the synthesis of a task-specific ionic liquid is the source of the functional group that is to be incorporated. Key to success here is the identification of a substrate containing two functional groups with different reactivities, one of which allows the attachment of the substrate to the core, and the other of which either is the functional group of interest or is modifiable to the group of interest. Functionalized alkyl halides are commonly used in this capacity, although the triflate esters of functionalized alcohols work as well. 

The Novartis group used the X-ray structure of a Grb2-peptide complex [68] as the structural basis for a design attempt that yielded entirely new non-peptide SH2 domain ligands [164]. As mentioned several times throughout this contribution, the interaction of the pTyr sidechain and the Asn sidechain in pTyr+2 position of the peptide ligand have been identified as key elements for molecular recognition (see Fig. 10). The obvious relevance of these two sidechain functionalities allowed the definition of a minimal pharmacophore pattern that... 

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