Infra Red Spectra

Task: Generate and Display the IR spectrum of nitro cyclopentadiene (). 

Time: 7 minutes

We built this molecule in the Fragment Library tutorial. The geometry must be optimized before starting.

1. Open the optimized file: File|Open "nitrocyclo-PM5".
2. Generate and tabulate the IR Spectrum.
1. Select Experiment|New.
2. Select:
1. Property of: Chemical Sample
2. Property: IR transitions
3. Using: MOPAC PM5 FORCE
4. Click Start.
3. The calculation window opens.  Information about the progress of the experiment scrolls in the window.  When the calculation is done, it will say "Tabulation complete".
4. Save the molecule after the calculations are complete.
5. Save the file: File|Save
3. Visualize the spectrum. 
   1. Open the file if necessary (File|Open nitrocyclo-PM5)
   2. Select Analyze|IR Transitions. 
   3. A screen with the IR transitions appears. Select Tile from the Window menu to view the spectrum and the molecule (with the motion vectors indicating the direction of movement for each atom).
   4. If your nitrocyclo molecule does not fit in the window, select View|Fit in Window from the menu bar.
   5. Chose the the Select tool, , and click on a transition indicated by a triangle in the spectrum window.
   6. The transition will be highlighted in red to show that it is selected. The motion vectors will be displayed in the structure window. 
   7. Select the structure window (click anywhere in the workspace).  Select View|Lines only from the View menu. It will be easier to view the vectors this way. 
4. Close the Windows.  Select No when asked if you wish to change the settings.

This is the end of the module on spectral properties.  In the next tutorial module you will compute properties that will allow you to predict chemical reactivity.