Viewing Vibrational Frequencies in HyperChem

Viewing Vibrational Frequencies in HyperChem

(HyperChem Version: 7)

Download The Files Associated With This Example
Input File Output File Formatted Checkpoint File
HyperChem: .pdb File Script File

HyperChem has the ability to display animations of vibrational frequencies much like the other programs discussed.  However, HyperChem does not have the ability to directly read any Gaussian file formats. Therefore you must use one of the Gaussian utilities to convert the checkpoint file before you will be able to use HyperChem to visualize the frequencies.

We will use “FreqChk” to format the checkpoint file from the frequencies calculation in Gaussian.  To do this:

  • Open Gaussian 03
  • Select Utilities|FreqChk
  • Use the File Browser to navigate to the folder your checkpoint file was stored in
    • Usually this is the Scratch folder in the G03 Directory
  • Select the checkpoint file resulting from the frequencies calculation and click OK
  • After you select the checkpoint file, a command line window will open, and display “Write HyperChem Files?”
    • Type “Y”
  • Another prompt will appear saying “Do you want to use the principle isotope masses [Y]?”
    • Type “Y”
  • Note that it would appear a formatted checkpoint file works when you use the FreqChk utility, but if you generate the HyperChem files using a formatted checkpoint file, they will not open properly in HyperChem

Viewing the Files in HyperChem

  • Open HyperChem
  • Select Script|Open Script
  • Use the File Browser to find the script file created with FreqChk and click OK
    • This should be located in the G03 directory named “freqchk.scr”
  • A new window will appear titled Vibrational Spectrum
  • The default display will be in wireframe.  If you wish to change this, you can the rendering by clicking “Cancel” in the Vibrational Spectrum window and then going to Display|Rendering
  • You should also rotate the molecule to an orientation where you will be able to see the vibrations at this point.
  • Select a vibrational mode by clicking on it in the spectra
  • Select “Animate Vibrations”
  • Select your mode by selecting it in the graph, or typing in it’s number in the field on the left of the window.  Then click Apply.
  • You can modify the animation by changing the numbers in the “Animation Cycle” window.
    • You can change the displacement of the atoms by changing the number in the Amplitude field.
    • To Change the speed of the animation, change the number in the Frames field.  More frames will slow the animation down, less frames will speed it up.
    • Click either Apply or OK
  • To stop the animation at any time, click Cancel in the Menu bar.

Saving the Vibrations as a Webpage

  • After the script is loaded select File|Save as HTML
  • In the window that opens, you can select what will display on the webpage.
  • The files generated by HyperChem can then be displayed online as a webpage.
  • You will need to download the HyperChem Web Viewer Plugin to view the COW files online.  It is available on the HyperCube website by clicking the link on the left titled Products, Free Software, and Demos.

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