Specifying R-groups

An R-group can contain atoms, variable atoms, shortcuts (functional groups), or fragments.

Note: An attachment point may be added to an R-group node.

 

  1. Click the R-group    tool. The R-group Definitions dialog box appears.

  1. Define an R-group using the methods described below. Note: Non-fragment R-group definitions will match what is set in Preferences.

Select an R-group (e.g., R1).

Select one or more atoms from the Atoms periodic table menu.

Select one or more variables from the Variables menu. (If necessary, click the arrow to open the Variables section.)

Select one or more structure shortcuts from the Shortcuts menu. (If necessary, click the arrow to open the Shortcuts section.)

Select one or more structure fragments from the Fragments menu. (If necessary, click the arrow to open the Fragments section.)

Fragments are drawn in the Structure Editor window and attachment points are assigned using the Fn    tool. A fragment cannot have more than two attachment points.

Or, type the symbols into the R-group field, separated by commas.

  1. To assign an R-group to the query structure, click the R-group (e.g., R2) in the R-group Definitions dialog box, and then click the atom site on the core structure.

  1. Repeat Step 3 until all the R-groups are assigned, and then click the X in the upper-right corner.

  Notes:

  • The generic groups Ak, Cb, Cy, and Hy are not allowed in rings or in R-groups that are placed in rings.

  • A maximum of 20 R-groups can be defined and included in a structure and an R-group can contain a maximum of 20 atoms, shortcuts, variables, or fragments.

  • The R-group designation (e.g., R2 ) appears in the Current Atom box and becomes the default atom until changed.

  • A fragment cannot have more than two attachment points.

 

Learn More

Drawing and Editing Structures

Substructure Queries

Reaction Queries