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.
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.
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.
Threshold
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.
Priority
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
Example:
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.
Example:
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.
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.
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.
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
From the Rules
menu, select the Add Molecule
command.
In the file dialog,
select a *.mol file.
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.
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.
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.
A new interpretation rule can be added by clicking with
the Left
mousebutton into the empty
row (next to the asterisk symbol) of the chemical classification rule
table on the bottom right of the:
A new row is inserted automatically and all values are
defined as (Null):
Enter valid
values into each column now or
select from the drop down boxes if applicable.
After leaving the current row with RETURN-key or by clicking with the Left
mousebutton, the interpretation
rule is updated.
A interpretation rule can be modified by clicking
with the Left
mousebutton into the desired field to be changed in the interpretation
rule table.
Enter new valid
values for the field or select
from the drop down boxes if applicable.
Leave the current field with the RETURN-key or by clicking with the Left
mousebutton into another
field. The interpretation rule is updated automatically.
icon or 
icon respectively.
