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Displaying Structural Fragments inside a Spectrum View

Basic molecule view functions are also applied here, but some additional functions are required for IR/RAMAN Spectrum Analysis. Here, structural fragments need to be displayed according to investigated functional groups. Molecule fragments are shown and they might have undefined residuals representing an unknown rest of a molecule. It is also possible, that more than one structural representation is available for a functional group. In this case each molecule fragment can be displayed alone or all can be shown together.

A typical Imine molecule fragment view looks like this. It represents all kinds of molecules containing an Imine functional group.

Contents of the molecule view are updated on selection of spectrum analysis results.

Atom Placeholders and undefined Residuals

As described above some residuals or atoms in the molecule fragments might be undefined in order to give a representation of a chemical environment for a set of various molecules. In Chemistry some well known abbreviations for such atoms or residuals are given in the following:

  • Alkyl Groups
    Alkyl-groups are indicated by a super atom "€œR"€.

  • Aromatic Groups
    Aromatic residues are represented by "€œPh"€ for phenyl or "Ar" for general aromatic residual.

  • Any Generic Groups
    Generic groups, either alkyl, aromatic, cyclic or non-cyclic, etc. are represented by "G"€.

  • Halogen Atoms
    Halogen atoms are indicated by "X"

Molecule View Display Options

Some functional group representations cannot be depicted by only one particular molecule, but a set of various molecule fragments representing all possible chemical environments. In this case multiple molecules are displayed in the view:

The navigation toolbar in the top left corner provides convenient control of visible molecule items. It will be shown automatically, whenever more than one molecules is displayed and the molecule view is activated or the mouse pointer resides in the view. The toolbar will be shown for navigation purposes. The molecule view offers two display modes:

  • Overview Mode
    All available molecules are visible at once.

  • Single View Mode
    Only one molecule is visible and maximized to the molecule view. The user can toggle between all available molecules.

View mode can be altered clicking the button in the navigation toolbar. Single view mode and overview mode will be toggled.

In the single view mode, only one molecule is displayed at a time. In order to toggle between all available molecules, move forwards and backwards in the list of all molecules clicking the and the buttons

  • Previous
    Shows previous molecule.

  • Next
    Shows next molecule.

Displaying Functional Groups in a Spectrum View

In the spectrum interpretation result, a molecular representation of the active functional group is displayed in the spectrum view:

All functions described above are also available for the molecule item shown inside a spectrum view.

  • Click with the Left mouse button onto the molecule in the spectrum view to activate and select the molecule item.

  • Move the molecule item around in the spectrum view with Drag & Drop.

  • Resize the molecule display by dragging and dropping the tracker symbols.

  • Click somewhere outside the molecule item to leave selection.

  • Click the Right mouse button to customize molecule view preferences.

 

The toolbar toggles the display mode...

Whenever the molecule display is selected, the toolbar is visible to customize display mode.

Customizing the Molecule View

Some preferences can be adjusted for the molecule view. Please refer to the chapter "Molecule View Preferences" for details.