Introduction
Axial stereoisomerism (atropisomerism) representation in CDD Vault
Registering Pure Enantiomers with Unknown Absolute Configuration
Registering a Series of Duplicates with Unique Registration IDs
Instructions for creating Brackets within Chemical Drawing Packages
Mixture Registration
Introduction
In general, molecules registered into CDD Vault containing “up” or “down” bonds are interpreted "as drawn". You can, however, represent racemic mixtures, pure enantiomers (both known and unknown configurations) using the V3000 enhanced stereochemical notation.
This annotation allows for registration of a single entity to describe stereochemical mixtures. The alternative method to draw two or more enantiomers, leading to registration of multiple entities in a single record with properties reflecting the total number of all molecules. This may lead to confusion since the fully drawn mixture of two entities would double the molecular mass. Using AND/OR annotations to register a single entity, will lead to expected molecular mass of only the one compound.
Here we demonstrate some implementations of these "AND" and "OR" enhanced stereochemical labels/designations.
As pointed out elsewhere in our Knowledge Base, stereochemical information is best dealt with as MOL (alt. SDF) format, instead of SMILES format due to the limitations of SMILES, especially with regards to mixtures. Therefore, we recommend drawing and registering a Molecule using the V3000 Enhanced Stereochemistry. Use the "AND" enhanced stereo label to indicate that the Molecule represents an isomeric mixture and the “OR” label to indicate cases for absolute, but unknown stereochemical centers.
With the Structure Editor in CDD Vault, users can select the atom and use the Stereochemistry tool from the top toolbar to add the labels. Note: You may also use the Alt-E keyboard shortcut after selecting the atom.
Once you've chosen the Stereochemistry tool, the Enhanced Stereochemistry menu will display. Here, you may select which label you wish to apply, AND or OR.
Below we illustrate several examples to help users with visibility/understanding of registered compounds using these labels. This should also allow the otherwise difficult to achieve registration of sterically hindered amides, or other, non-tetrahedral chiral structures.
The following represents a mixture of 4 diastereoisomers
and represents a mixture of all of the following 4 diastereoisomers
The following represents a mixture of 2 enantiomers
and represents a mixture of the following 2 enantiomers
The following represents a mixture of 2 enantiomers
and represents a mixture of the following 2 enantiomers
The following represents a pure sample of unknown configuration
but is one of these 4 diastereoisomers
The following represents a pure sample of unknown absolute configuration
but is one of these 2 enantiomers
The following represents a pure sample unknown configuration
but is one of these 2 enantiomers
Registering Pure Enantiomers with Unknown Absolute Configuration
To register pairs of enantiomers when the absolute configuration is unknown:
1) For the first isomer:
- Draw a wedge (up) bond for the stereocenter .
- Select the stereocenter and click the stereo tool from the top toolbar (or click Alt-E).
- In the dialog box, select “Create new OR Group".
- Click the Apply button.
2) For a second isomer, repeat the process for the first isomer with a hash bond at the stereocenter.
3) When you register the second isomer, you will get the message below at the top the page. Scroll down below the Strip and Stoichiometry radio buttons and select New molecule. A new molecule ID will be assigned.
This allows you to register the racemate, both unknown configurations and both known configurations of this molecule as separate entities:
Axial stereoisomerism (atropisomerism) representation in CDD Vault
CDD Vault supports the registration of compounds containing Axial stereoisomerism (atropisomerism), which is a stereochemical assignment resulting from hindered rotation around a single bond when the isolation of individual conformer is possible.
Atropisomers can be drawn with wedged and hashed bonds within the aromatic rings and directly connected to the single bonds about which they rotate. This common atropisomer representation using wedged/hashed bonds in aromatic systems is used by the registration system for the purposes of duplicate detection. For example, these two molecules will be seen as two unique molecules by our registration system:
However, edge cases can occur where two atropisomers are not recognized as unique. To distinguish between them and override the automatic duplicate detection, two special S-Groups, "atropisomer" and "override", can be added to bonds or atoms.
Method
If I have registered this structure...
... and now want to register the other atropisomer but I am getting a second batch of DEMO-1000234 automatically created, I should:
- open the Ketcher Structure Editor,
- draw or insert the structure,
- click on [S+] on the left toolbar, and
- click on the stereo bond.
In the S-Group Properties pop-up dialog box, I would then:
- fill in the "Field name" box with the term, "atropisomer" (this "atropisomer" Field name has to be lowercase!), and
- fill in the "Field value" box with a unique value for this structure
The new structure now contains a bond that's annotated with the "atropisomer" label that contains the value provided, and will register into CDD Vault as a new, separate Molecule.
Helpful Hints:
- enhanced stereochemistry notation ("or" & "and") can be used with atropisomer registration
- We also have another data s-group called "override" (without quotes) that can be used for a similar purpose and is meant to be used for cases beyond atropisomerism.
Registering other chiral compounds as unique molecules
Example: Axial chirality (non-tetrahedral chiral compound)
In the case of axial chirality, we suggest using the data S-group ([S+) workflow with the 'override' field name.
For helicene type of compounds you would register them in the same way.
The important feature to remember for this type of registration is the usage of the Field Name = override functionality.
Instructions for creating Brackets within Chemical Drawing Packages
If you are in need of generating duplicate registrations for 2 to 4 molecules, users can create the molecules using CDD Vault's built in chemistry editor, Ketcher. Here are the steps:
1) Draw the first molecule in Ketcher and Register the structure.
2) For the first duplicate (molecule 2), draw the molecule again in Ketcher. Select the portion of the molecule where the Repeating Group should appear. Click the "S Group" icon on the left toolbar.
Fill in the details in the S-Group Properties dialog box.
3) For the 2nd duplicate (molecule 3), Repeat Step 2 and change the top pull down box to "Head-to-head". Register the molecule.
4) For the 3rd duplicate (molecule 4), Repeat Step 3 and change the top pull down box to "Either unknown". Register the molecule.
** Note - Most chemical properties will not be calculated with the structure created using this S-Group Properties menu.
If you are in need of generating more that 4 duplicate registrations, you will need to use a 3rd party chemical editor (like ChemDraw).
For ChemDraw v18, here are the steps to create molecules with different bracket combinations:
1) Draw the molecule
2) Click the "Brackets" icon on the main toolbar. Extend the bracket so the entire molecule is within the bracket.
3) Mouse over the bracket and right click. Select Bracket Usage, then "Monomer". Right click again and select Repeat Pattern then "Head to Tail"
Our current testing should allow users to register up to 32 copies (duplicates) of the same molecule using the following combinations of Bracket Usage and Repeat Pattern.
1) Base Molecule
2) Ketcher - Repeating Groups - ht, n=1 OR ChemDraw 18 - Bracket Usage = SRU, n=1 - Repeat Pattern = Head to Tail (default)
3) Ketcher - Repeating Group - hh - n=1 OR ChemDraw 18 - Bracket Usage = SRU, n=1 - Repeat Pattern = Head to Head
4) Ketcher - Repeating Group - eu - n=1 OR ChemDraw 18 - Bracket Usage = SRU, n=1 - Repeat Pattern = Either/Unknown
** Note - Most chemical properties will not be calculated with the structure created via these workflows.
5) ChemDraw 18 - Bracket Usage = Monomer - Repeat Pattern = Head to Tail (default)
6) ChemDraw 18 - Bracket Usage = Monomer - Repeat Pattern = Head to Head
7) ChemDraw 18 - Bracket Usage = Monomer - Repeat Pattern = Either/Unknown
8) ChemDraw 18 - Bracket Usage = Component - Repeat Pattern = any
9) ChemDraw 18 - Bracket Usage = Co Polymer - Repeat Pattern = Head to Tail (default)
10) ChemDraw 18 - Bracket Usage = Co Polymer - Repeat Pattern = Head to Head
11) ChemDraw 18 - Bracket Usage = Co Polymer - Repeat Pattern = Either/Unknown
12) ChemDraw 18 - Bracket Usage = Copolymer Alternating - Repeat Pattern = Head to Tail (default)
13) ChemDraw 18 - Bracket Usage = Copolymer Alternating - Repeat Pattern = Head to Head
14) ChemDraw 18 - Bracket Usage = Copolymer Alternating - Repeat Pattern = Either/Unknown
15) ChemDraw 18 - Bracket Usage = Copolymer Block - Repeat Pattern = Head to Tail (default)
16) ChemDraw 18 - Bracket Usage = Copolymer Block - Repeat Pattern = Head to Head
17) ChemDraw 18 - Bracket Usage = Copolymer Block - Repeat Pattern = Either/Unknown
18) ChemDraw 18 - Bracket Usage = Copolymer Random - Repeat Pattern = Head to Tail (default)
19) ChemDraw 18 - Bracket Usage = Copolymer Random - Repeat Pattern = Head to Head
20) ChemDraw 18 - Bracket Usage = Copolymer Random - Repeat Pattern = Either/Unknown
21) ChemDraw 18 - Bracket Usage = Crosslink - Repeat Pattern = Head to Tail (default)
22) ChemDraw 18 - Bracket Usage = Crosslink - Repeat Pattern = Head to Head
23) ChemDraw 18 - Bracket Usage = Crosslink - Repeat Pattern = Either/Unknown
24) ChemDraw 18 - Bracket Usage = Generic - Repeat Pattern = Head to Tail (default)
25) ChemDraw 18 - Bracket Usage = Generic - Repeat Pattern = Head to Head
26) ChemDraw 18 - Bracket Usage = Generic - Repeat Pattern = Either/Unknown
27) ChemDraw 18 - Bracket Usage = Graft - Repeat Pattern = Head to Tail (default)
28) ChemDraw 18 - Bracket Usage = Graft - Repeat Pattern = Head to Head
29) ChemDraw 18 - Bracket Usage = Graft - Repeat Pattern = Either/Unknown
30) ChemDraw 18 - Bracket Usage = Modification - Repeat Pattern = Head to Tail (default)
31) ChemDraw 18 - Bracket Usage = Modification - Repeat Pattern = Head to Head
32) ChemDraw 18 - Bracket Usage = Modification - Repeat Pattern = Either/Unknown
Other bracket notations may be available in ChemDraw that has not be tested and could result in even more duplicate molecules.
Mixture Registration
For registration of mixtures (multi-compound) structures, please visit these articles
Single Registration of Chemical Entities
Is it possible to add structures to structureless molecules