ACD/Name
Generate Name from Structure

V. STEREOCONFIGURATIONS

V.1. General Policy

ACD/Name treats only chiral centers and configuration of double bonds. Other types of chirality (axial, planar, helical) are not supported. The current version of ACD/Name can generate only descriptors of the following types:

• R/S description for chiral stereo centers;
• E/Z description for double bonds;
• exo/endo and syn/anti for bicycles where common R/S descriptors cannot be assigned;
• cis/trans for monocycles and bicycles with two pseudochiral centers;
• r/s description for pseudochiral stereo centers (only for IUPAC naming); and
• α/β and cis/trans descriptors in natural products.

R/S-descriptors for structures with chiral P, As, and S atoms.
E/Z-descriptors for double bonds in cyclic systems.

For example:

IUPAC Name	(1R,3R)-1-methyl-3-{[(2E)-2-methylbut-2-en-1-yl]oxy}cyclopentane
Index Name 11.0	cyclopentane, 1-methyl-3-[[(2E)-2-methyl-2-buten-1-yl]oxy]-, (1R,3R)-
Index Name 10.0	cyclopentane, 1-methyl-3-[[(2E)-2-methyl-2-butenyl]oxy]-, (1R,3R)-
IUPAC Name	(3-exo,8-anti)-8-methylbicyclo[3.2.1]oct-6-en-3-ol
Index Name	bicyclo[3.2.1]oct-6-en-3-ol, 8-methyl-, (3-exo,8-anti)-

Note: Any stereo site to which ACD/Name can't assign a stereo descriptor is treated as non-stereo and stereo descriptors are not assigned.

Note: The way stereodescriptors are cited by Index Name varies in some cases from that recommended by CAS Index Nomenclature rules. The user can disable the citation of stereodescriptors in the Preferences dialog box. The descriptors generated by ACD/Index Name that have been explicitly cited can be used for manual construction of the desired stereoconfiguration term.

V.2. Absolute, Relative and Racemic descriptors

ACD/Name preferences allow users to specify the way in which to cite stereodescriptors for structures with chiral centers. The structure can be named as having absolute, relative, or racemic configurations.
For example:

Stereoconfiguration Preference
	IUPAC Name	Index Name
Ignore	hept-5-ene-2,3-diol	5-heptene-2,3-diol
Absolute	(2R,3S,5E)-hept-5-ene-2,3-diol	5-heptene-2,3-diol, (2R,3S,5E)-
Relative	rel-(2R,3S,5E)-hept-5-ene-2,3-diol	5-heptene-2,3-diol, (2R,3S,5E)-rel-
Racemic	rac-(2R,3S,5E)-hept-5-ene-2,3-diol	5-heptene-2,3-diol, (5E)-

Note: The way the stereodescriptors are cited by ACD/Name implies absolute, relative or racemic relations for all chiral centers in a structure.

V.3. Stereo Drawing Conventions

3D Structures

ACD/Name recognizes configurations of chiral centers and double bonds in structures with 3D coordinates. Stereo bonds in such structures are not necessary and are ignored to avoid contradiction.
For example:

IUPAC Name	(1S,2R,4R)-1-bromo-2,4-dimethylcyclohexane
Index Name	cyclohexane, 1-bromo-2,4-dimethyl-, (1S,2R,4R)-

2D Structures
There is no single way to define stereo configuration in 2D structure drawings, especially if it involves directed stereo bonds - "up" and "down" wedge bonds. Different drawings can change the generated stereo descriptors and as a result the whole name.

Stereo bonds	Down	Up
Directed
Undirected	and

The current version of ACD/Name allows the user to choose between two possible procedures of wedge stereo bond analysis by choosing the appropriate option of Stereo bond direction in the Preference dialog box.

Undirected Stereo Bonds
If "ignore" is chosen the sign ("up" or "down") of the stereo wedge will not depend on the direction and all stereobonds will be analyzed as undirected: hashed bonds are down bonds and solid bonds are "up".
For example:

Wedge bond direction Ignore
IUPAC Name	(2R)-2-chlorobutane	(2R)-2-chlorobutane	(2R)-2-chlorobutane
Index Name	butane, 2-chloro-, (2R)-	butane, 2-chloro-, (2R)-	butane, 2-chloro-, (2R)-

Note: Undirected stereobonds are not coded in MDL *.mol and *.sdf file formats and are replaced by wedges.

Directed stereo bonds
If "take into account" is chosen, the "up" and "down" wedges will be analyzed with regards to their directions (depending to which atom a narrow end is attached).
For example:

Wedge bond direction Take into account
IUPAC Name	(2R)-2-chlorobutane	(2S)-2-chlorobutane	(2R)-2-chlorobutane
Index Name	butane, 2-chloro-, (2R)-	butane, 2-chloro-, (2S)-	butane, 2-chloro-, (2R)-

Note: For ignored direction, any stereo bonds are not allowed between two chiral centers.
Undirected stereo bonds are also not allowed between two chiral centers in any case.

V.4. Depth of Comparisons in Stereo Assignment

The ACD/Name level of depth of ligands' comparison is 10. When comparing the seniority of four ligands at any stereo center (and for two pairs for double bonds), the algorithm takes into account the neighbors of the atom under investigation. First, the direct neighbors of the center are taken into account; if there are no differences in the first sphere, then the next level is analyzed for seniority, and so on until the 10^th sphere. If two ligands do not differ within ten spheres they are treated as equal and corresponding stereo center as non-chiral.