Software Wedge Conventions:
ACD/Name, ChemDraw,
AutoNom and Nomenclator *
(a part of ACD
Inc. presentation draft)
The existence of several stereo drawing conventions results in conflicts between user specification and computer interpretation of drawn structure stereo configuration. The lack of agreed conventions makes an each software developer to choose their own way independently. This restricted survey compares stereo bond conventions of four programs, ACD/Name, AutoNom, Nomenclator and ChemDraw that allow to generate stereodescriptors for drawn structures [1].
The table below illustrates the generated descriptors and bond analysis for four possible situations with the wedge between stereo and non-stereo center. Four available descriptor generating products stick to some extent to the concept of directed stereobonds, which means that analysis of stereo wedges depends on their direction.
|
|
ACD/Name |
ChemDraw |
AutoNom |
Nomenclator |
|
|
R(up) |
R (up) |
R (up) |
R (up) |
|
|
R or S (up or down) 1 |
S (down) |
- |
S (down) |
|
|
S (down) |
S (down) |
S (down) |
S (down) |
|
|
S or R (down or up) 1 |
S (down) 2 |
- |
R (up) |
1 ACD/Name allows to switch between two ways of analysis: take into account wedge direction or ignore.
2 ChemDraw analysis of down wedge direction depends on the number of substituents at connected atoms
|
|
|
|
|
|
|
Descriptor |
S (down) |
S (down) |
S (up) |
R (down) |
In the table below the analysis of stereo bond between two stereo centers by four programs is represented. In each cell the generated descriptors and bond sense are shown corresponding to to the order of atoms (left to right)
|
|
ACD/Name |
ChemDraw |
AutoNom |
Nomenclator |
|
|
refuse |
R,S (up, up) |
no such bond |
R,S (up, up) |
|
|
S,S (down, up) |
S,S (down, up) |
-,S (no, up) |
S,S (down, up) |
|
|
refuse |
S,R (down, down) |
no such bond |
S,R (down, down) |
|
|
R,R (up, down) |
R,R (up,down) |
-,R (no, down) |
R,R (up, down) |
It is quite obvious that undirected stereo bonds such as lines or bars are really ambiguous if drawn between two stereo centers. It seems very important to mention that the most simple and common to exchange structure information MDL (MDL Information Systems Inc.) mol file format doesn’t support undirected stereo bonds and while exchange of drawn structural information through a mol file format wedges replace such bonds. More over, the drawing with broken bar will be converted by software into a structure with wedges of hardly predictable direction (most common with narrow end to the atom with lower internal numbering).
The number of ways to designate stereoconfigurations and needed decisions for each case, obviously leads to the differences between programs in the way of analysis. But the most impressive part of this comparison is that the differences are really minor and all four mentioned programs agree in general in two points:
· the analysis of stereo wedge depends on its direction and
· the wedge type corresponds to its “color” for the atom at the narrow end of stereo wedge.
We may conclude that chemical software developers, apart from practicing chemists and publishers, are quite close in the analysis of stereoconfiguration designations and analysis.
All mentioned inconsistencies in the interpretation of drawn stereoconfiguration lead to dangerous population of chemical literature and electronic information sources with ambiguous and even incorrect information. More over, this process is accelerating by the growing degree of software utilization in chemistry. It is obvious that the whole chemical community hardly can once switch to “chemical software convention” but the discussion and publication of a recommended conventions will help both chemists and software developers to avoid mistakes and misinterpretations.
* the mentioned software:
ACD/Name, Advanced Chemistry Development Inc., Toronto, Canada,
ChemDraw Ultra, CambridgeSoft Corporation, Cambridge, USA,
AutoNom, MDL Information Systems (formerly Beilstein Informationssysteme GmbH), Frankfurt, Germany,
Nomenclator module of Chemistry 4D Draw, ChemInnovation Software, Inc., San Diego, CA, USA,
http://www.cheminnovation.com/
