# Isotopic labeling

To study molecular structure in a larger system, it is helpful to move some local mode frequencies away from the others and see how the spectral features change.[^isotope] For vibrational spectroscopy, this can be done by substituting the atoms within the interested modes with their isotopes. For example, $^{12}C$ can be replaced by $^{13}C$ in amide-I vibration modes. This modification usually reduce the local mode frequencies.

To simulate the spectral effect of the isotopic labeling, COSMOSS allows users to manually modify the 'label index' and their shifted frequencies in the Model_GUIs.

Let's use the 'Model TCO' as an example:

In the 'Local mode setting' panel, the 'Labeled Freq.' specifies the shifted frequency while the 'Label Index' specifies which oscillators will be modified. In this example, I modify the first modes with the local mode frequencies equal to 1630 $cm^{-1}$. Here is the comparison between the non-labeled and the labeled spectrum:


You can see a little peak appears around 1620 $cm^{-1}$ due to the isotopic labeling.

You can also modify multiple modes at once. Let's try to label a few local modes using 'Model PDB Amide-I' with two labels:

Or combine with the array notation:

Note, you can toggle on/off the 'Label' option in the 'Figure options' panel to view the modification.

[^isotope]: https://en.wikipedia.org/wiki/Isotopic_labeling
###### tags: `tutorials` `COSMOSS`