To see how a reaction structure query works, you will draw this Diels-Alder reaction, and then search Current Chemical Reactions^® for reactions that either match it or have it as a substructure.

Drawing the Reaction

From the Reaction Search page, click the Draw Query button inside the Reaction Query box to go to the Structure Drawing program.

Step 1 - First Reactant

1. Click the Pencil tool to select it.

2. Click the double bond tool at the bottom of the screen.

3. Position the pointer (shaped like a pencil) inside the window towards the left edge. Hold down the mouse button and drag upwards to draw the bond. Then release the mouse button. Since a reaction has not been defined yet, the fragment is labelled any role.

Step 2 - Second Reactant

1. Select the Chain tool.

2. Make the chain length 4.

3. Click once in the center of the drawing window to draw the chain.

4. Select the Pencil tool again.

5. Inside the dialog box, click the button next to Double, and then click Multiple Use. The current bond will be a double bond until you change it again.

6. Click the two bonds that need to be double bonds. Notice how the pencil displays a line when it points to a bond and displays an A when it points to a node.

Step 3 - Product

1. Press the spacebar to reset the current bond to single.

2. Select the Ring tool, and then click OK to accept a 6-membered ring.

3. Click once in the drawing window to draw the ring.

4. Select the Pencil tool again. Click the double bond button once at the bottom of the window, and then click the bond that should be changed to a double bond on the ring.

5. Select the Lasso tool if you need to reposition any structure.
   
   Hold down the mouse button and then draw a circle around the structure you want to move. Now click inside the circle. Notice the hand inside the circle. Drag the mouse to move the structure.

Step 4 - Add the Reaction Arrow

1. Select the Reaction Arrow tool, and then click OK in the box to accept the default arrow.

2. Position the arrow pointer between the second and third structures. Drag the mouse horizontally to draw the arrow.

Notice that now two structures are labelled reactant and product.

Step 5 - Assign Reaction Roles

A structure on the screen can be searched as a reactant or product or either (any role). To define a role:

1. Select the Reaction Role tool.

2. Click any atom or bond on the first structure.

3. Click the Reactant button in the dialog box, and then click OK. Now the structure is labelled reactant.

Step 6 - Map Atoms from Reactants to Products

Map atoms from reactants to products. Reactions can be mapped manually or automatically.

1. Select the Mapping tool.

2. In the dialog box, select Manual Mapping, and then click OK.

3. Click the first carbon in the first reactant, and then click the corresponding carbon in the product. Use the Diels-Alder reaction as a guide. After you click the corresponding atom, a number appears on both reactant and product.

4. Continue to map all the atoms in the reactants and product as shown. Notice that the numbers appear directly above the nodes they're attached to.

Step 7 - Query Definition

1. Click the Pencil tool to clear the mapping mode.

2. Click on the toolbar to bring up the Query Attributes window. As you move the pointer over each atom or bond, watch the values inside the window change. You define query attributes through the Query Def/Attributes menu.

3. Click again or click the Close box on the Query Attributes window.

Executing the Search

1. From the Structure Drawing window, select Back from the Search menu to transfer the drawing to the Reaction Search form.

2. Select the kind of reaction search you want: Substructure or Exact Match.

3. You can also add compound or reaction data to your search by entering in the appropriate areas on the form.

4. Click the Search button to execute the query.

Saving a Structure Query

1. From the Structure Drawing window, select Save Query from the Search menu. The Save Query dialog box appears.

2. In the dialog box, navigate to the folder where you want to store the query, and then enter a name for the file. The saved structure file has the extension .str.

3. Before you save the structure, you will get the opportunity to modify it.

4. Click Save to save the structure.

5. Once the file is saved, you can add it to the Search form for searching, create additional structure drawings or close the Structure Drawing window.

Modifying a Structure Query

This query retrieved reactions whose reactants are part of chain structures, not rings. You can modify the query to specify that the reactants match both chain and ring structures. This will expand your search to include reactants such as cyclopentadiene or furan.

To modify a saved reaction structure:

1. From the Chemical Search page, click the Draw Query button inside the Reaction Query box to go to the Structure Drawing program. The Draw Query button opens a new window. To find the reaction you've just drawn, close the new window. You should see the Diels-Alder reaction in a window underneath.

2. Click the Selection tool, and then draw a box around both reactants. (Place the pointer above and to the left of the reactants. Then drag downward to the right.)

3. Select Node Characteristics from the QueryDef menu.

4. Select Chain, and then click OK.

5. Now define the bonds of the selected reactants as Ring or Chain by selecting the Bond Characteristics option from the same menu.

6. Specify exact for the bond value. The query structures will match only reactants with the corresponding double bonds. Click OK.

7. Select the product and make the bond type ring and the bond value exact.

8. While you could use the Query attributes button again to check your query as before, instead use the Query Verification button. This option lets you check the attributes for the entire reaction.

9. Click OK to verify all attributes. A dialog box appears containing the name of an attribute.

10. Click OK to move to the next attribute. As you move through the attributes, the relevant atoms or bonds are highlighted.

11. Click Cancel to exit the Query Verification dialog box.

Tips on Using Reaction Sites

Often it is useful to specify reacting sites in a reaction. For example, in this bromination reaction, the atoms are mapped, and the Reacting Site tool is used to highlight position 5 on both reactant and product. This will retrieve substitution reactions.

If position 5 on the reactant is not marked as a reaction site, then both addition and substitution reactions are retrieved.

Process Flow

1. Drawing the Reaction
2. Executing the Search
3. Saving a Structure Query
4. Modifying a Structure Query
5. Saving a Reaction Structure Query
6. Tips on Using Reaction Sites

Information About ...

• Atoms and Bonds
• Sample Reaction Query
• Tool Palette
• Toolbar Buttons
• Using the Structure Drawing Plug-in