Abstract Representation of Molecules

Sometimes, molecules are represented as Markush stmctures in a generic context to cover a family of molecular structures which can go beyond millions [62], Markush structures are generic structures used in patent databases such as MARPAT main- 

Markush stmctures are used in patents, combinatorial library generation, depiction of polymers, etc. 

ChemAxon provides plugins for generating Markush stmctures from a given library of molecules (Fig. 1.28). 

The Markush viewer is another module to view R group definitions of a molecule in a hierarchical graphical form. It classifies scaffolds and R groups in a given molecule file. The markush stmcture of aspirin molecules is shown here with R1 and R2 group definitions (Fig. 1.29). 

Markush stmcmres can be enumerated efficiently irsing command line options. The cottunand line syntax is cxcalc randottunarkushenirmerations -f sdf -C 2 t5000 filename.mol and the output can also be piped to Marvin dew. In the current version of the program. Instant JChem can be used to determine the Markush space density of a patent molecule. 

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Lewis structures are drawn by representing each valence electron by a dot. These dots are transformed into vertical arrows if it is necessary to show electron spin. Eixceptions are the Is electrons, which are held too tightly to be importantly involved in bonding except in hydrogen. These electrons are not shown in Lewis structures except in H and He. Somewhat more abstract representations of molecules are made by showing electron pairs in bonding orbitals as lines— the familiar bonds between atoms. 

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