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Defining
Substructures
To define a substructure:
1. Build a model of the substructure. You can use
Chem3D tools, or build it in the ChemDraw
panel.
2. Select the atoms to define.
3. From the Edit menu, choose Copy.
Select atoms 3-5 (the two oxygens and the carbon
between them) and using the instructions above,
create a new record in the Substructures Table.
If you want to append an ester onto the end of the
chain as a carboxylic acid, you can simply
double-click a hydrogen to replace it with the ester
(as long as the name of the substructure is in the
text box). Replacing H(8) (of the original structure)
would produce the following structure:
To save the substructure definition:
1. Open Substructures.xml. From the
2. View menu, point to Parameter Tables and
choose Substructures.
3. Right-click in the Substructures table and
choose Append Row.
A new row is added to the table.
4. Select the cell in the Model column.
5. Right-click in the cell and choose Paste from
the context menu.
The structure is pasted into the table cell. Note
that it will be not be visible until you move to
another cell.
6. Select the cell in the Name column.
7. Type a name for the substructure.
8. Close and save the Substructures table.
For example, consider an ester substructure,
R 1 COOR 2 . You can build this substructure as part
of the following model:
Notice that the carbon atom in the ester has
replaced the hydrogen. This is because, when the
ester was defined, the carbon atom had a lower
serial number (3) than the oxygen atom that formed
the other attachment point in the substructure (5).
NOTE: When defining substructures with multiple
attachment points, it is critical to note the serial numbers of
the atoms in the substructure so that you can correctly orient
the substructure when it is inserted in the model. See the rules
for multiple attachment points discussed at the beginning of
this section.
614• Substructures CambridgeSoft
Defining Substructures