You can create correspondences between atoms in different structures to use in
creating queries to search reaction databases. The reactions mapped can be
single or multi-step. You can assign atom-to-atom mapping creating records for
a reaction database and for creating queries to search reaction
The mapping algorithm perceives and assigns a reaction center for the reactants
When a reaction map is established, you can point to an atom in one structure
with the reaction atom-atom map tool selected to highlight the mapped atom in
the other structure. Atom mapping can be assigned in two ways:
- Automatic mapping
Draw the reaction you want to map and select reactants and products. Click the
map reaction atoms command on the structure menu. The symbol Rxn appears next
to the bonds in the reactant and product that are perceived by the
algorithm as being modified by the reaction. These symbols are bond properties
that are automatically applied.
See diagram on the left, where the number 1 indicates the atoms that are
- Manual mapping
In situations that require manual mapping of atoms, you can use the reaction
atom-atom map tool
A-->A on the main tool palette. This might be necessary when the automatic
mapping is applied to complicated reactions, and gives incorrect results. In
these cases you can manually readjust the reaction mapping.
diagram on the right, you must indicate which atoms you want to map.
Note: Preferences.ShowReactionMap must be true, to make the symbols
appear and print on the atoms when reaction mapping has been performed