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Designing Molecules for a Functional Group

It is easy to draw molecules like benzene with an external structure editor but molecules suitable for use in functional groups is more difficult.

An external molecule editor is required!

Any free or commercial structure editor can be used to create molecule files in the *.mol file format.


Functional groups are meant to be parts of such molecules. From the functional group point of view, it is a molecule residual. In the interpretation rule database these molecule fragments are used to identify a functional group within an  analyzed molecule. For this purpose, the residual part a molecule fragment is attached to needs to be well defined according to the allowed chemical environment.


A carboxylic acid functional group is shown in the following, which might be attached to any residual molecule:

In the corresponding functional group definition, the molecular fragment needs to be assigned. Furthermore, the unknown residual (indicated by the question mark) needs to be specified in more detail. This is useful to distinguish e.g. aromatic from aliphatic carboxylic acids. In case of aromatic carboxylic acids, the residue must be an aromatic compound, but it would never be any aliphatic compound like an Alkyl-group. Therefore, residuals (indicated by the question mark) will be considered as Generic atoms with special properties. These properties can be defined in the atom property dialog (see below).

Workflow for Designing a Functional Group Molecule

To design a functional group molecule, please follow the instructions below:

  1. Open the external structure editor and draw the functional group of interest.

  2. Replace any open residual by an R atom.

Example: Carboxylic acid molecular fragment

  1. Save or export the drawn molecule file (*.mol or *.sk2).

  2. Select the destination functional group node in the tree of the Rule Designer.

  3. From the MS-Windows explorer, drag the molecule file (*.mol or *.sk2) and drop it onto the molecule section of the Rule Designer:


  4. Double click with the Left mouse button onto the R atom within the molecule view to edit the Generic atom properties.

  5. An Atom Properties dialog is opened, where generic atom properties according to the SMILES and SMARTS nomenclature can be adjusted. Please refer to the "Generic Atom Properties" section for details.

  6. After modifying the atom properties, close the dialog clicking the button.