CDD Vault Update (June 2021): Representation of Unknown, Pure Enantiomers within CDD Vault

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June 8, 2021

 Jungian author James Hollis once wrote, “Learning to live with ambiguity is learning to live with how life really is, full of complexities and strange surprises.” CDD Vault has taken an important step towards handling chemical registration complexities with an enhancement designed to handle the registration of unknown, pure enantiomers.

When registering multiple Molecules that are pure stereoisomers where the stereochemical configuration of each Molecule is unknown, the structures can be drawn using the enhanced stereochemical OR label. When the OR stereo label is used to represent multiple enantiomers, they are often considered to be duplicate structures by chemical registration database systems.
However, when specifically using the OR stereo label, CDD Vault will allow these “duplicate structures” to be registered as separate, distinct Molecules (assigned unique Molecule IDs).
As an example, you may now register multiple unique Molecules to represent different pure enantiomers:

Manual Structure Registration

To manually register these enantiomers, navigate to the Explore Data tab, select the “Create a new… Molecule” button and then “Launch the structure editor”. Now, draw your stereoisomer, being sure to use the OR enhanced stereo label.

Now, repeat the “Create a new… Molecule” process using the same structure containing an OR enhanced stereo label. You will be notified that the “Structure already exists” and advised to “indicate below whether you want to register a new molecule or a new batch of an existing molecule.”
At this point, scroll down to the bottom of the “Structure” section and select the desired radio button:

  • create a “New Molecule”, or
  • add a new Batch to an existing Molecule (the enantiomer previously registered).
Select New Molecule

When choosing the “New Molecule” radio button, the duplicate structure drawn will be registered in CDD Vault as a separate, unique Molecule and assigned a new Molecule ID.

Bulk Structure Registration

When using the Import Data wizard to register new Molecules and Batches, you will be presented with an Ambiguous Event whenever a duplicate enantiomer containing the enhanced OR label is detected.

Clicking on the “View details” link will expand the Ambiguous Event panel and allow you to select the desired “Resolution”:

  • create a “New Molecule”,
  • add a new Batch to an existing Molecule (the enantiomer previously registered), or
  • reject the row so that the enantiomer will not be registered.

Once you’ve made your selection, remember to click the blue “Apply” button and finally click the green “Commit Data Import” button.

Helpful Hints

1. CDD Vault will use the number of OR stereocenters to determine how many total unique enantiomers are allowed to be registered as separate, unique Molecules.
2. For additional documentation, please see the “Registering Pure Enantiomers with Unknown Absolute Configuration” section of the “Advanced Stereochemistry Registration” Knowledgebase document.
3. For additional information on stereogenic centers drawn using an OR n group (e.g. OR1) to represent stereoisomers that are either the structure as drawn OR the epimer in which the stereogenic centers have the opposite configuration, please see ChemAxon’s documentation.