Structure searching in SciFinder

From WolfWikis

To work with chemical structures in SciFinder Scholar, from the home screen, click Explore, then Chemical Structure. This opens the structure editor for drawing and editing structures. Numerous shortcut tools are available for drawing. See CAS help for details on specific tools.

• Check the vertical palette (pictured at right) help to get help with the structure drawing tools.
• Check the horizontal palette (picture below) help to get help with the atoms and bonds tools.

Structure drawing has been called an art! It can be challenging. Note that you don't have to make it look beautiful, just get the pieces in the right relative places.

Types of substance searches

After completing your drawing, you can utilize three types of searches for substances. You can also search for reactions.

Exact Search

An search for precise structure entered in the editor. Allows for only very minor variation.

Substructure Search

Less rigid than the exact search, this option returns chemicals in which the entered structure is a portion of the overall structure.

Similarity Searching

Even less rigid than the substructure search, this option returns anything similar to the entered structure, ranked by similarity.

Reaction Searching

Reaction searching is done by making use of the Reaction Arrow Tool.

After drawing a structure, select the Arrow and click and drag to place it. Pointing the arrow away from the structure automatically assigns a Reactant/Reagent role to the chemical. Pointing the arrow towards the structure assigns a Product role, as show here:

You can change the default assignment with the Reaction Role Tool.

Click Get Reactions to conduct a search, and change any variables or filters that are applicable.

Putting a known structure in the structure editor

Figure 1. In versions prior to 2007, copy the CAS number, not the structure. Confusing!

Chemical structures can be drawn using the available tools, or opened (if saved previously). For substructure and similarity searching, it is often helpful to copy and paste a known structure from search results as in this process.

1. From the home screen, click Locate
2. Click Substance Identifier
3. Enter the CAS number, name, or other identifier of the known substance, click OK.
4. Click the structure in the results, then click Explore by Chemical Structure.

To send a known structure to the structure editor in SciFinder Scholar versions prior to 2007 takes a few more steps:

1. From the home screen, click Locate
2. Click Substance Identifier
3. Enter the CAS number, name, or other identifier of the known substance, click OK.
4. Highlight (or triple-click) the CAS number (NOT the structure iteslf--this is counterintuitive) and click Edit--Copy. (See Figure 1.)
5. Go back to the home screen by clicking the New Task button.
6. Click Explore
7. Click Chemical Structure
8. Click Edit--Paste. The structure should appear in the drawing window.
9. Click Get Substances
10. Select Similarity Search and any filters you are interested in.
11. Check the boxes corresponding to the results you want to see and click Get Substances.

Saving work in the structure editor

It may be helpful to save your drawings in the structure editor, since it can be a time-consuming process. Use File--Save to do so. SciFinder supports several formats. Notably:

• .cxf - the default structure file format in SciFinder Scholar.
• .mol - a more universally-recognized file format for chemical structures. The Isis/Draw program used by the Crossfire Commander software (i.e., Beilstein) uses .mol