User guide

Cahn-Ingold-Prelog
Absolute stereochemistry is calculated for tetrahedral atoms and double bonds according to the Cahn-Ingold-Prelog
(CIP) priority rules.
The CIP rules are designed to order ligands by their priority and determine a descriptor based on the orientation of the
ordered ligands in space.
A ligand is an entity attached to a stereocenter. For example, a tetrahedral carbon has four ligands corresponding to its
four substituents. When a tetrahedral carbon is in a ring, it still has four ligands: the two ligands outside the ring, a third
consisting of the ring “unpeeled” clockwise, and a fourth consisting of the ring “unpeeled” counterclockwise.
Five rules used to determine the priority of ligands are summarized below in simplified form. For more detailed infor-
mation, see the references.
Rule 1. Higher atomic number precedes lower
Rule 2. Higher atomic mass precedes lower
Rule 3. cis precedes trans
Rule 4. Like pairs of descriptors precede unlike pairs
Rule 5. R precedes S
ChemBioDraw 13.0 checks differences up to 15 atoms distant from the stereocenter.
Stereochemical indicators
After the ligands are ranked, an indicator is assigned as shown in the following table.
Stereocenter Indicator
Double bond
Z if the highest ranking ligand of each pair are on the same side of the bond; otherwise E.
Tetrahedral atom
When the lowest-ranking ligand is located behind the central atom:
R when remaining 3 ligands are arranged clockwise in descending order
S when remaining 3 ligands are arranged counterclockwise in descending order
r or s is used for pseudo asymmetric atoms
Stereochemical flags
While the chirality of a specific stereocenter can be indicated with the appropriate wedged, hashed, or plain bond,
sometimes it is useful to indicate the relative stereochemistry of a molecule as a whole, considering the relationship
between all stereo-centers. Stereochemical flags apply to the nearest structure; if no structure is within the distance
specified by the Fixed Length value, the stereochemical flag is not assigned to any structure.
ChemBioDraw 13.0
Chapter 15: Chemical interpretation 296 of 401