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One of the second order corrections involves the automatic recognition of molecular symmetries: internal and external symmetry and optical isomers. Symmetry is inherently based on the three dimensional structure. However, the information available to JTHERGAS is a molecular graph. The three dimensional information has to be inferred and assumptions have to be made. This is a design decision that has to be made when creating the database for symmetry structures.
As with the rest of JTHERGAS, the philosophy of the implementation of symmetry recognition is that all information in the recognition process is within the extendable database. There are basically two pieces of information that are needed, the generalized structure with unspecified ligands and a table specifying the properties of the ligands.
The key to the symmetry recognition process is to match (atom-atom correspondences) the symmetry structure within the target molecule and then identify the substructures corresponding to the unspecified atoms. For example, in the, the carbon in the general structure can be matched with all the carbons in propane. For the match with C2, the middle carbon in propane, a and b can be matched the the hydrogens and c and d can be matched with the methyl groups. Due to the symmetry of the system, there are 4! (4*3*2*1) or 24 ways to match the unspecified atoms with the center carbon of propane. For the symmetry determination, the information is condensed to that the carbon has two sets of two matching groups, i.e. the set with hydrogens and the set with the methyl groups. For external symmetry, it is also important that the hydrogens, being single atoms, are considered to be linear structures and that the methyl groups have a symmetry of 3.
One of the second order corrections involves the automatic recognition of molecular symmetries: internal and external symmetry and optical isomers. Symmetry is inherently based on the three dimensional structure. However, the information available to JTHERGAS is a molecular graph. The three dimensional information has to be inferred and assumptions have to be made. This is a design decision that has to be made when creating the database for symmetry structures.The generalized procedure can be said to be:
1. Match the symmetry structure within the target
2. For each match, identify the groups attached to each of the unspecified atoms (labeled R in the example).
3. Identify which ligands are the same and group them together.
4. Identify the symmetry of each group or whether the group is linear or not.
5. Condense this information into a table of groups where each group has the number of equivalent ligands and the symmetry or linearity of ligand.
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