Chem3D 8.0 Manual - CambridgeSoft

AdministratorDefining SubstructuresTo define a substructure:1. Build a model of the substructure using theBond tools and the Text Building tool.2. Select the atoms to define.3. From the Edit menu, choose Copy.To save the substructure definition:1. From the View menu, choose theSubstructures table.The Table Editor opens and the Substructurestable becomes the active window.2. From the Edit menu, choose New Compound.3. Select the hyphen to the right of the name, in theModel column.4. From the Edit menu, choose Paste.5. Select the cell in the Name column.6. Type the name of the substructure.7. Close the Substructures table.8. Click Save.For example, consider an ester substructure,R 1 COOR 2 . You can build this substructure as part ofthe following model:3. From the View menu, choose theSubstructures table.The Table Editor opens and the Substructurestable becomes the active window.4. From the Edit menu, choose New Compound.5. Select the hyphen to the right of the name, in theModel column.6. From the Edit menu, choose Paste.7. Select the cell in the Name column.8. Type “RCOOR” for the name of thesubstructure.To save the substructure:1. Close the Substructures table.2. Click Save.Suppose you want to insert an ester elsewhere in thechain.To insert the ester between C(6) and C(7):1. Select the Text Building Tool.2. Click the C(6)-C(7) bond.3. Type RCOOR in the text box and press Enter.The C(6) - C(7) bond is deleted. Additionalhydrogens are added to both C(6) and C(7) ifthe Automatically Rectify check box in theBuilding control panel (Chem 3D Setting dialogbox) is selected.To define the substructure:1. Select C(3), O(4) and O(5).2. From the Edit menu, choose Copy.To insert the ester substructure:1. Shift-click one of the hydrogens bonded to C(6)and one of the hydrogens bonded to C(7).2. Press Enter.C(6) and C(7) are separated and the estersubstructure is inserted.A2 • CambridgeSoftDefining Substructures