Vibrational Normal Mode Analysis Dialog Box

Analyze normal modes from a selected range of a UV/Vis band shape spectrum for animation in the Workspace.

To open this dialog box, click the Vibrational Normal Mode Analysis button in the Spectrum Plot Panel.

  • Using
  • Features
  • Additional Resources

Using the Vibrational Normal Mode Analysis Dialog Box

This dialog box is used to perform an analysis of the vibrational modes that contribute to a specified region of a band shape UV/Vis spectrum. The object is to find parts of the molecule that are vibrationally excited during the electronic transition. The analysis generates information for the vibrational modes of the initial and final electronic states, and presents the information separately for each state. The ground vibrational state is ignored in the analysis, so there may be no information produced if all the contributing vibrational modes are in the ground state for either or both of the electronic states. The information is used to animate the vibrations in the Workspace using the Vibrations Panel.

The main choice to be made is whether to show all contributing modes, an average of the contributing modes, or the most intense of the contributing modes. The amplitudes of the vibrations displayed via the Vibrations Panel can be weighted by the average vibrational quantum number found for each of the modes in the specified region.

The region of the spectrum is marked by two vertical green lines, which can be dragged to adjust the range of the spectrum included in the analysis. When you click OK, the vibrational data are written out along with the structure, and imported into the Project Table as a new entry group labeled normal_mode_analysis. The group can contain zero, one, or two entries, depending on whether there is vibrational excitation in the initial or final state, both or neither. The entry titles begin with "initial" or "final" for the analysis of initial and final electronic state vibrational modes, and include information about the analysis. Each entry has a V button so you can view the animation in the Vibrations Panel. By default, this panel opens with the data from the first entry group when you click OK.

Vibrational Normal Mode Analysis Dialog Box Features

Energy window start text box

Reports the start of the energy window in which the normal modes are selected for analysis. This value represents the excitation energy at the right green vertical line in the spectrum plot, and changes when you drag this line.

Energy window stop text box

Reports the end of the energy window in which the normal modes are selected for analysis. This value represents the excitation energy at the left green vertical line in the spectrum plot, and changes when you drag this line.

Normal modes to animate menu

Choose which normal modes to animate via the Vibrations Panel:

  • All—animate all modes: each mode is separately included in the Vibrations Panel. The amplitudes in the animation are weighted by the average vibrational quantum number if Include effects due to vibrational quantum number is selected.

  • Average—display one vibration that is an average over the normal modes in the energy window, weighted by their Huang-Rhys factors. This option allows you to view the vibrational motion of the atoms in the molecule as a whole, and thus determine which atoms are moving most in the chosen region of the spectrum. No account is taken of the amount of vibrational excitation, by default. If Include effects due to vibrational quantum number is selected, the normal modes are weighted by the average vibrational quantum number as well.

  • Maximum—animate the mode that has the maximum intensity (Huang-Rhys factor, multiplied by the average vibrational quantum number if Include effects due to vibrational quantum number is selected).

Include effects due to vibrational quantum number option

When calculating amplitudes for display of the normal modes, weight the amplitudes for each mode by the average of the vibrational quantum numbers found for that mode in the analysis region.

Reset button

Reset the dialog box to its default settings, clearing all data.

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