Reaction Searching Tips

Reaction searching in Beilstein CrossFire/Commander can sometimes lead to hitsets containing very large numbers of reactions, many of which are often not of current interest. There are a number of techniques you can use to reduce the number of irrelevant hits in a reaction query. These directions for advanced reaction searching assume a basic knowledge of reaction searching in Beilstein CrossFire/Commander. If you need documentation for a review of basic reaction searching techniques, try Beilstein General Guide (Daresbury) or consult the online help in CrossFire.

1. Draw your reactant and product molecules in the Structure Editor using Editmode/Structure. Switch to Editmode/Reaction using the menu bar at the top of the screen.
2. Specify reactant(s) and product(s) by highlighting the structure(s) (use lasso or select ) and using the appropriate grouping buttons (Reactant or Product).
3. Still in Editmode/Reaction, click on the pencil tool.
4. Draw a "bond" between the desired atom in the reactant and the target atom in the product. You may repeat this step with another atom pair, but don't do more than a couple or you will slow down your search.

Figure 1 below shows what an atom map looks like when steps 1 through 4 are complete:

Figure 1. Atom mapping in reaction searching

This technique can be used especially effectively when you want to specify a particular substructure or functional group to undergo a reaction while the rest of the molecule remains the same. To specify a particular bond breaking and/or making reaction, follow these steps.

1. Draw your reactant(s) (and/or product) in Editmode/Structure. Switch to Editmode/Reaction using the menu bar at the top of the screen.
2. Specify reactant(s) and/or product(s) by highlighting the structure (use lasso or select ) and using the appropriate buttons (Reactant or Product).
3. Still in Editmode/Reaction, click on the pencil tool.
4. Line up pencil tool over the bond of interest and click. The Bond Box should appear (figure 2).
   
   
   Figure 2. Selecting break/make bond in Reaction Searching

5. Click on the small box near the lower right hand corner labelled "Break/make bond". A small check mark should appear. Click OK

As an example, suppose you were looking only for ring opening reactions of substances of the type below in Figure 3:

Figure 3. Cyclic amide structure

You could run the reaction search without specifying a particular bond cleavage. The resulting answer set would be 409 reactions, many of a type not including ring opening. For an example, see Figure 4.

Figure 4. Sample result for non-restricted reaction query

On the other hand, if you specify bond cleavage of the carbonyl carbon-nitrogen bond, the answer set is only 24 reactions, of the type shown in Figure 5.

Figure 5. Sample result for reaction query including specific bond cleavage/creation

You can also specify that a particular bond or bonds NOT be involved in the reaction. Simply follow the steps for Bond Making and/or Breaking, but in Step 4, click the "Do not change" box.

Specifying a Non-Graphical Reactant (i.e., Reagent)

While reagents are not written as part of the reaction in the structure window in Display Hits, they are searchable in the Fact Editor. This can be done in combination with the results of a structure based reaction query to limit the number of hits in some very large answer sets. An example illustrating this approach is given here.

The reaction query should be constructed first in the Structure Editor, using atom mapping, free site designation, reactant/product definition and/or bond make/break definitions as usual. After the reaction query is constructed and is run in the Beilstein Commander window, a hitset with a Q-number designation (i.e., Q01, Q02, etc.) will be generated. This Q-number can be combined with other search terms in the Fact Editor.

To use a Q-number set, first identify the appropriate Q-number from the Beilstein Commander main window (see Figure 1).

Figure 1. Finding the Q-number for a hitset

Then start the Fact Editor and create the reagent specific query as follows:

1. Enter the Q-number preceded by a period (.) in the first data box under the heading Field Labelin the Fact Editor form (should look like .Q01).
2. Enter the Boolean operator AND in the first data box under the heading Operator
3. Click the cursor in the next data box under the heading Field Label.
4. Check for the correct code for "reagent" using the List Values button (see Figure 2).
   
   
   Figure 2. List Values button in Fact Editor

5. Click the Find button, then type in reagent. When the correct term in the data hierarchy is highlighted, click OK and the correct data label (i.e., rx.rgt will be transferred into the box in the Fact Editor (see Figure 3).
   
   
   Figure 3. Using the Find feature to identify correct search label

6. To get the correct value for the reagent "name", click in the box for Value.
7. When the dialog box appears, start typing the reagent name or symbol, in this case "socl2". This will move you through the alphabetically index of terms appearing in the rx.rgt field in the Beilstein database. When you see a term that matches the reagent of interest, click on it to highlight it and then click OK. The value will be transferred to the Fact Editor form. (See Figure 4).
   
   
   Figure 4. Using the Find feature to identify the correct reagent "name"

Figure 5. Reaction with SOCl2 as reagent highlighted

Andrea Twiss-Brooks, Chemistry Librarian/Chemical Information Specialist
University of Chicago
atbrooks@midway.uchicago.edu