Online Software Help Manual

Display Legacy Contents

Rule Designer

Functional groups of chemical compounds cause one or more related peaks at known positions in an IR or RAMAN spectrum. In research the analyst takes measured spectra and tries to find prominent bands. Assignments need to be matched to suggested or known molecules. For a detailed introduction, please also refer to the chapter "IR/RAMAN Analysis Overview".

The main target of the rule designer is defining interpretation rules and organize them in a spectroscopic manner. Interpretation rules represent the encoded knowledge of an experienced spectroscopist.

In the rule designer, interpretation rules can be created, modified, deleted, copied and pasted and administered. The dialog looks like this:

Interpretation Rule Tree

The interpretation rule tree view (in the left part of the figure above) shows the organizational structure of rules within the interpretation rule database. Rules can be organized following a particular hierarchy:

Chemical Class

The chemical class is an organizational instance, which collects all characteristic properties of a group of substances, e.g. alcohols or aromatic hydroxy compounds.

Chemical Sub-Class

The chemical sub-class is an organizational instance like the chemical class itself. In some cases, the chemical class is too general and needs to be split into several sub-classes, e.g. the chemical class aromatic hydroxy compound is divided into the sub-classes Aromatic Alcohol and Phenol.

Functional Group

Each chemical class or sub-class contains a number of functional groups corresponding to a fragment in a molecule. These functional groups in a molecule are responsible for a collection of characteristic bands in a spectrum.

Interpretation Rule

Each IR or RAMAN band is represented by an interpretation rule. It is the smallest available unit in the interpretation rule database. Properties of a band have been computerized into several parameters describing the band shape and characteristics.

Navigation in the Rule Data Base Tree

The following operations are available in the tree view on the left of the dialog:

Expanding and collapsing Tree Nodes

Nodes in the tree can be expanded and collapsed by clicking with the Left mouse button on the icon or icon respectively.

Selection of Tree Nodes

Selection of a functional group node automatically updates the interpretation rules table and the molecule view accordingly.
If a chemical class or sub-class is selected, the views and tables are cleared.

Multiple Selection of Tree Nodes

By holding down the CTRL-key and selecting several nodes in the tree, more than one node can be selected. This feature is useful on copying and pasting several functional groups.

Adding a new Functional Group, Chemical Class or Sub-Class

A new item (chemical class, sub-class or functional group) can be easily inserted into the tree.

  1. Just select the node, where the new item must be inserted.

  2. Press the INS-key to insert the next lower level item below the selected node.

  3. Type a name for the new item into the highlighted new node and press the RETURN-key to finish.

Removing Tree Nodes

An item can be easily removed.

  1. Select the node of the item, which has to be removed.

  2. Press the DEL-key.

  3. Confirm the message by clicking the Yes button.

Renaming Tree Nodes

An item can be renamed as described in the following:

  1. Select the node of the item, which has to be renamed.

  2. Press the F2-key.

  3. Type a new name for the item into the highlighted node and press the RETURN-key to finish.

  4. To cancel this operation, press the ESC-key.

Copy and Paste Operation for Functional Groups

Functional groups in the tree can be copied and pasted to another item, e.g. chemical class or sub-class.

  1. Select the one or more functional group nodes, which has to be copied.

  2. Press the CTRL-C-keys to copy it into the clipboard.

  3. Select a destination chemical class node or sub-class node in the tree.

  4. Press the CTRL-V-keys to paste the functional groups.

Interpretation Rules Table

Each functional group is characterized by a set of interpretation rules being listed in the table on bottom right of the dialog. They possess the following properties:

Vibration Name

This is meant to be a user defined name for the IR band describing the vibration type, e.g. O-H stretch or O-H bend.

Start Wave Number

This is the starting wave number of the interval, where the experienced analyst would expect the band in a spectrum. Values need to be entered in 1/cm units.

Stop Wave Number

This is the ending wave number of the interval, where the experienced analyst would expect the band in a spectrum. Values need to be entered in 1/cm units.

The range will be used in spectrum interpretation...

The spectral range of an IR and RAMAN band defined by start and end wave number is used in band recognition during spectrum interpretation. Some manual fine tuning might be done in the Preferences. If the range is not clearly defined, an overall deviation should be defined there before starting a spectrum interpretation.


The threshold describes the expected intensity of an IR or RAMAN band. The intensity is given in the categories listed below relative to all peaks in the analyzed spectrum. The following categories are available:

  • Very weak

  • Weak

  • Medium

  • Strong

  • Very strong

  • Variable
    Variable means, the intensity strongly depends on the chemical environment and spans from very strong to very weak.

This parameter will be used in spectrum analysis...

The threshold is used in IR and RAMAN band recognition during spectrum analysis. Some fine tuning of the categories is done in the Preferences. The threshold values for those categories should be adjusted properly, before starting a manual spectrum interpretation.


The priority of a band describes the relative importance of the IR band. Sometimes bands are very weak or will be rarely observed because of the chemical environment or other experimental conditions. By experience of the analyst the importance of an IR band must be estimated applying the following categories:

  • Very low (green colored)

  • Low (green colored)

  • Medium (green colored)

  • High (green colored)

  • Very high (green colored)

  • Excluded (red colored)
    This option has an extra meaning, which overrides the interpretation of other rules in the functional group, if the condition is met. It allows to exclude a particular IR band from a functional group


If a carboxylic acid is analyzed, strong signal at approximately 1690 1/cm is available for the carbonyl group and a strong signal is available at approximately 3500 1/cm for the OH-group. In the definition of an alcohol functional group, the analyst would never expect a carbonyl band, although he would expect a OH-band. Therefore in definition of the alcohol functional group, the carbonyl band should be excluded. In this case, the functional group would be ignored in analysis.

  • Mandatory (yellow colored)
    This option has inverse meaning to excluded. It overrides interpretation of other rules in the functional group, if the condition is met. It allows to include a particular spectral region as mandatory in a functional group. At least one peak must be available in this region to match the condition.


    Regarding the example from above, if a strong signal at approximately 1690 1/cm for the carboxylic acid group is missing, this would never be a carbonyl group, although other bands might match the settings in the functional group definition. In this case, the functional group should be ignored in analysis.

Coloring of Spectral Regions 

The bands are color encoded according to their priority to allow quick identification:

  • Green Color
    All expected bands are green colored. The degree of transparency indicates the priority. Opaque bands possess high priority. The more transparent they get, the less is their priority.

  • Yellow Color
    All mandatory bands are yellow colored.

  • Red Color
    All excluded bands are red colored.

Molecule Fragment View

On top of the dialog, the actual functional group is presented as molecule fragment. The molecule is shown in a molecule view. Please refer to the chapter "Molecule View Functions" section for details.

Add or replace a Molecule in Functional Group

One or more molecule fragments can be added to a particular functional group. They need to be drawn with any commercial structure editor in advance and provided as *.mol file to the software. The following methods are available to add a molecule to a functional group:

  • Drag and drop a *.mol file from windows explorer to the spectrum view on top of the dialog.

  • Add a Molecule command

    1. From the Rules menu, select the Add Molecule command.

    2. In the file dialog, select a *.mol file.

    3. Click the Open button to add the molecule.

How to develop molecules which can be used in Functional Groups.

In the rule designer functional group molecules need a special Shape, because the algorithm used for Validating spectrum and molecule will analyze provided molecule itself for available functional groups. Here the molecules of each functional group definition will be matched with the molecule provided in validation. This matching algorithm requires special definitions for generic groups and super atoms.

Please refer to the chapter "Designing Molecules for a Functional Group" for details.

Spectrum View with Interpretation Rule Placeholders

The spectrum view shows the position of interpretation rules within the visible spectral range as colored rectangles. The color encodes the priority of a particular spectral region.

Please refer to the chapter "spectrum view functions" for details.

Show the position of chemical classification rules on a sample spectrum...

For some applications, it is required to see the position of chemical classification rules of a functional group directly on an underlying spectrum. For this purpose, a spectrum file (*.spc) can be directly dragged and dropped as layer onto the spectrum view from MS-Windows explorer.


Modification of Functional Groups

A basic set of interpretation rules and corresponding hierarchy is provided with the installation of the software. You may modify, add or remove functional groups and molecules yourself to improve and adapt the rule database to your personal requirements. For this purpose, the following options are available:

Changes will directly change all interpretation results!

Modification of the rule database will take direct effect on your interpretation results. Please be careful when modifying interpretation rules.


Changes will be stored automatically!

Changes will be stored, if the rule designer is closed. You will be prompted to confirm saving modifications.

Adding a new Interpretation Rule to a Functional Group

  1. A new interpretation rule can be added by clicking with the Left mouse button into the empty row (next to the asterisk symbol) of the chemical classification rule table on the bottom right of the:

  1. A new row is inserted automatically and all values are defined as (Null):

  1. Enter valid values into each column now or select from the drop down boxes if applicable.

  2. After leaving the current row with RETURN-key or by clicking with the Left mouse button, the interpretation rule is updated.

Modifying a Interpretation Rule of a Functional Group

  1. A interpretation rule can be modified by clicking with the Left mouse button into the desired field to be changed in the interpretation rule table.

  2. Enter new valid values for the field or select from the drop down boxes if applicable.

  3. Leave the current field with the RETURN-key or by clicking with the Left mouse button into another field. The interpretation rule is updated automatically.

Deleting a Interpretation Rule from a Functional Group

  1. With your mouse point to the dark blue area in front of a row within the interpretation rule table.

  2. Click the Left mouse button to select the row in the table.

  3. Press the DEL-key to delete the row.

  4. Confirm the warning message with the Yes button.