Pipette Sketcher and Stereochemistry

Last Updated: Nov 08, 2015 09:31PM PST

Summary: This article explains how Pipette Sketcher handles stereochemistry and provides background information about the three types of stereochemical groups (ABSOLUTE, OR, and AND).

Covered Topics

Clicking a link will scroll the page to the relevant section.

Stereochemistry Concepts

BIOVIA's enhanced stereochemical representation introduces three types of identifier that can be attached to a stereogenic center. Each stereogenic center that is marked with wedge bonds belongs to a stereochemical group. Grouping allows us to specify stereogenic centers with a relative relationship. We can also use grouping to specify more than one relative grouping of stereogenic centers.

The only restriction on the number of stereogenic center collections is that a stereogenic center can be a member of solely one stereochemical group. The three types of stereochemical groups are called ABSOLUTE, OR, and AND.

The ABSOLUTE group replaces the chiral flag, which is no longer used in the enhanced system of representation. Instead of applying the chiral flag to the structure, you specify that all stereogenic centers that are marked with wedge bonds are members of the ABSOLUTE group. Stereogenic centers that are not part of the ABSOLUTE group must belong to an OR or an AND group.

Characteristics of the different types of stereochemical groups are described in the following table.

Stereochemical Identifier Represents
ABSOLUTE Stereogenic center where the absolute configuration is known.
OR Stereogenic center where the relative configuration is known, but the absolute configuration is not known.
AND Mixture of stereoisomers; can be a pair of enantiomers or all the diastereomers.

The OR group is equivalent to a relative representation and the AND group is equivalent to a racemic representation. Either of these representations can be applied to a single stereogenic center.

In the case of the OR group, the meaning is a structure that represents one stereoisomer that is either the structure as drawn (R,S) OR the epimer in which the stereogenic centers have the opposite configuration (S,R). The relationship can be between samples rather than within the structure.

Note: For further information, see the Biovia Enhanced Stereochemical Representation white paper http://accelrys.com/products/pdf/enhanced-stereochemical-representation.pdf

Set the Stereochemistry Flag for a Stereo Center in Pipette Sketcher

Pipette Sketcher allows you to control all aspects of the stereochemistry of a compound.

To set the stereochemistry flag for a stereo center:

  1. Draw the compound and the stereo centers.
  2. Select a stereo center.
  3. Configure it as one of the following:
  • Absolute center (ABS)
  • OR center (or)
  • AND center (&)

Pipette Sketcher will add the appropriate labeling based on these flags.


Common Types of Stereochemistry Supported by Pipette

The following is a list of the most common types of stereochemistry supported by Pipette.

Example Description
ppt_stereochemistry_single_pure_isomer.png Single pure isomer with known absolute configuration


Mixture of isomers with unknown absolute configuration (either as drawn or the enantiomer).



Mixture of enantiomers


Either of two epimers


Mixture of epimers

Pipette Sketcher Overview

Pipette Sketcher Features and Structure Examples


seconds ago
a minute ago
minutes ago
an hour ago
hours ago
a day ago
days ago
Invalid characters found