Computational Chemistry at GVSU

Vibrational Frequencies of HCl and DCl

1. Build and clean HCl, and then do a quick AM1 geometry optimization to get the structure in a good starting geometry.
2. Enter Gaussian, set the the basis set to "6-31G(d)" and the method to "HF" (Hartree Fock).
3. Choose "Gaussian 94" and set the Job Control machine to "local host".
4. Under "File prefix", give the file the name "HClHF".
5. Determine the optimal geometry for HCl by performing a geometry optimization. Save this model as HCl.msi (Choose "File" in the top menu, and then "Save Model").
6. Measure the interatomic distance by clicking, in the top menu, "Geometry" and then"Measurement". Push the "Distance" button. Select the two atoms bordering the bond. Make sure your model is displayed in the "Stick" mode to see the distance. Record the equilibrium bond length in your notebook.

Determining the Normal Modes of HCl

7. What number of normal modes do you expect to find for HCl in 3-D space? ______

How many of these modes do you expect are

Translational?________

Rotational? __________

Vibrational?__________

8. Perform a frequency calculation by choosing "Frequency" instead of "Geometry Optimization" as the task. All frequency calculations must be performed from a stationary point, which in this case is the bottom of the potential energy well found via the geometry optimization. Note that the frequency calculation must always be done with the same method and basis set as the geometry optimization. Set the file name to "HClHFfreq".
9. Run your calculation.
10. Under "Analyze->", choose "Vibrations" to bring up the normal mode window. Put the appropriate scale factor in the bottom left box of the panel (see the table of scale factors handed out in class, or obtain the list on page 64 of Reference 1). Click the "Calculate" button at the top of the panel.
11. Click on each frequency, and select "Animate".
12. Do you have the number and kind of normal modes as predicted in 7. above? Record any vibrational frequencies in your notebook.
    
    

Creating a Potential Energy Surface Scan

13. Choose the "Potential Surface Scan" task in the Gaussian Run box, and choose "More" for this task. Select the variable "r2" (see the Z- matrix under Geometry in the Gaussian Card Deck for a definition of r2), and vary it from 0.8 Å to 2.0 Å in 20 steps. Call the file hclscan1 and click on "Run".
14. Repeat step 13., but rename the file to hclscan2 and change the scan to be from 2.1 Å to 4.8 Å in 10 steps. Run the scan.
15. Go to your folder on the desktop, and double click on hclscan1 and from hclscan2 to open them.
16. Next, from a UNIX shell window, type

    jot

    A window will come up, into which you will copy your scan data from the other two files, hclscan1 and from hclscan2, to make one large data set. Save the composite data as simply hclscan. (Your instructor can assist you if you need help.)

17. Cerius² doesn’t graph the resulting Gaussian electronic potential energy curve, so use a graphing program to plot Total Energy vs. interatomic distance. See your instructor for details. Examine the graph - does the plot display anharmonicity? Is a harmonic oscillator a good model for the diatomic dynamics? At what interatomic distances do you predict the harmonic oscillator model will no longer be accurate?

18. Load your geometry optimized model, HCl.msi, into a new model space. This should be the structure that resulted from the geometry optimization of HCl. Verify that the bond distance is the HCl equilibrium bond distance you recorded earlier. Highlight the hydrogen atom, and choose "Edit Atom" under the "Build" menu at the top of the control panel. Change the mass of the hydrogen to 2 and hit <ret> to create DCl. Check that the program did indeed switch the mass of the hydrogen to two by labeling the atoms by MASS (use the yellow selection tool under the main menu, which by default says "NO LABEL").
19. Which of the above steps do you need to repeat for DCl? Verify your answer with your instructor. Why don't we need to redo the potential energy surface?
    
    
    
    
20. Set the file prefix to "DClHF".
21. Set the Task to a Geometry Optimization & Frequency, to do both together as one task in cerius2. Make sure the method is "HF" (Hartree Fock) and the basis set is "6-31G(d)". Run the calculation.
22. Record the equilibrium bond length for DCl in your notebook. Does it differ from HCl? Is this expected?
    
    
    
    
    
23. Under "Analyze->", choose "Vibrations" to bring up the normal mode window. Put the scale factor 0.893 in the bottom left box of the panel. Click the "Calculate" button at the top of the panel. Record the vibrational frequency in your notebook. Did this change from the value for HCl? Is this expected?
    
    
    
    
    
    
    

Preparing for the Level Program

As a final step, we will use our potential energy surface scan to compute various vibrational and rotational parameters, which will be compared to the results from the wet lab. The program we will use is called Level, and directions on how to use this are given out in a separate handout. But first we need to compute the total energy of H and of Cl each.

24. Using Hartree-Fock (HF) and the 6-31G(d) basis set, calculate the total energy of an H atom alone and of a Cl atom alone. We’ll do this via a single point energy calculation. (Why is a geometry optimization unnecessary here? What spin multiplicity do you need?). Once you’ve run your single point energy calculation for hydrogen, choose "Analyze->", "Files", and scroll down in the window that pops up to find the total energy. This is the energy released when an electron and a proton come from infinity to form a hydrogen atom. Record this energy below, and then convert it to cm^-1 units.

Total Energy for H __________________________________

 

Total Energy for H in cm^-1 __________________________________

 

Repeat the above for Cl

Total Energy for Cl __________________________________

 

Total Energy for Cl in cm^-1 __________________________________

 

Add the two energies together.

Total energy of H + Cl in cm^-1 __________________________________

 

25. We will now copy a file from a different directory into our own, that we will then modify and use as the input file for the program Level.

In UNIX, the current directory you are in is given the shorthand name "." . Yes, that's a period. UNIX always tries to keep things simple if arcane. To copy a file to the current directory, in general the command is "cp filename ." . The file we want to copy is /usr/level/hcltemplate, so in a UNIX shell window (dark blue), type

cp /sgi/level/hcltemplate .    Note, this command ends in a space and then a period.

To edit the file, then type

jot hcltemplate

26. Find your folder on the right side of the desktop, double click on it to open it, and double click on the file that contains your scan data (hclscan). You should have two jot windows open, which you can copy and paste between.