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Using SciFinder: The Structure Drawing Editor

SciFinder is an entry to research from many scientific disciplines including biomedical sciences, chemistry, biochemistry, engineering, materials science, agricultural science, and more.

Structure Drawing Editor Functionality

The structure editor is used to build 2-dimensional drawings of molecules which can then be used to conduct a search against the SciFinder® database.

There are two structure editors to choose from: Java-enabled and non-Java enabled.  This choice is provided because of past concerns by some users relating to the computer security of Java-based applications.

While the structure editor works the same way, the drawing tools available vary depending on whether you have entered it by initiating a chemical structure search, a reaction structure search, or a Markush structure search.

 

Tips when Searching by Substructure

Judith Currano, Chemistry Librarian at the University of Pennsylvania, notes that searching by substructure is akin to searching text using truncation.  ". . . one enters a portion of a molecule into the search system and retrieves substances that contain that fragment, or 'substructure'."  (2014, p114)

Currano points out that the challenge to searching by substructure is developing a structure with an appropriate degree of specificity.  Depending on your goal, determines how detailed you draw the substructure and she notes that the art of substructure searching comes from "balancing the length of time spent constructing a search with the length of time one wants to spend evaluating the results (2014, p.115)" while a second challenge is guessing how the structure has been represented in the database (p.115).

Currano offers the following steps as a basic procedure for substructure searching:

  1. identify the portion of the molecule that is of interest.
  2. determine whether the stereochemistry, geometry, and bond order of each connection in the stucture is fixed or flexible.
  3. decide where and how your substructure may be further substituted.
  4. determine the topology of each atom and connection in the structure (p115).

She advises that the searcher to think like a database, rather than as a chemist and to think your structure through before beginning to draw it.

For more detailed information on thinking about and drawing substructures, see Chapter 5 of Chemical Information for Chemists: A primer.

REFERENCES

Currano, J. (2014).  Searching by structure and substructure.  In J.N.Currano & D.L. Roth (Eds.), Chemical Information for Chemists: A primer (pp.109-145). Cambridge,UK: RSC Publishing.

Structure Editor: Toolbars, Tools, and Menus

Working across the menu from left to right (see above), you have access to the following functionality for creating and editing structures:

  • start a new structure
  • import a structure (in CXF*) that you have perhaps exported previously or that has been sent to you.  Based on personal experience, it seems you need to be using the Java-enabled structure editor to import a structure and that the relationship between Java and the browser (e.g., IE, Chrome, etc.) can complicate the use of this functionality.
  • create a structure by using the CAS Registry, SMILES, or InChI number.
  • export a structure (in CXF*)
  • save a structure as a template**, helpful if you are going to be using it again.  These are stored in the USER-DEFINED folder of the Templates menu (on the Drawing Tools Menu).
  • print
  • cut
  • copy
  • paste
  • undo
  • redo
  • repaint**
  • check overlaps**
  • preferences

* CXF = Chemical Abstracts Exchange Format

** requires the Java-enabled structure editor.

This section, located at the bottom of the structure editor, presents some commonly used atoms, bonds, and ring structures. See also the atom, the short-cut, and variable menus.

The Drawing Tools (see illustration to the right):

The illustration to the right illustrates the full range of drawing tools available.  Those outlined in red are available when opting to draw a structure or Markush; those additional tools outlined in green are only available when drawing a reaction. 

The tools available include (based on each row of two tools):

  • draw (includes keyboard short-cut menu) and erase
  • the atom menu and the shortcuts menu.
  • the variables menu and the R-group definitions menu
  • the repeating tool group and the variable attachment point tool
  • the chain tool and the (pre-defined) structure templates
  • the selection tool and the (free hand) lasso--both for selecting portions of structure to be edited
  • the abilities to lock down a ring and to lock down a specific atom
  • the abilities to rotate the structure and to flip the structure
  • the abilities to add a positive charge or a negative charge
  • the abilities to add a reaction arrow and reaction roles*
    • the direction of the reaction arrow will determine if your structure is a product or a reactant
  • map atoms in a reaction and mark bonds to be formed or broken*
    • both are used to increase the specificity of your reaction search
  • choose a functional group*

*Reaction Editor only.

    

   

                                           

         Variables Menu

                 

                  R-group Definitions

Functional Groups (see illustration ot the right; accessible via the Drawing Tools menu -- see excerpt below) allow one to limit the possible results of a reaction search.  Each of the functional groups opens further to show the options available for each class of group.  Functional Groups may also be used to limit the reaction search by choosing that option through the "Advanced Search" of the Explore Reactions section of SciFinder®.

 

Tired of clicking?  Keyboard shortcuts can sometimes help.  This menu of "shortcut keys" are accessible from the main menu of the Structure Editor or by pressing "?" at any point.  To close the menu, click anywhere on the screen.

The actual menu of shortcuts include the following:

Tutorial

TUTORIAL:  Introduction to the NON-JAVA Structure Editor.  (~10 minutes.) You must be logged into SciFinder for this link to work.

TUTORIAL:  Introduction to the JAVA Structure Editor.  (~10 minutes.) You must be logged into SciFinder for this link to work.