Frequency analysis for BH₃

Important You can carry out these calculations on the laptop.

Now we are going to carry out a frequency or vibrational analysis to confirm we have minium structures. This MUST to be carried out on a fully optimised structure

Prepare an input file

• The first thing we need to do is to open the file from your 6-31G(d,p) BH₃ optimisation and save a copy to edit.
• From the main menu along the top of the screen (in Gaussview) choose "file" and then "open" from the pull-down menu, a new window will open with available files. before selecting a file first check that under "File type" the pull-down menu has "Gaussian Output Files (*.out *.log) selected. Also ensure you have the "Read Intermediate Geometries" tick-box un-checked!! Then click on the "open" button
• a new molecule window should open with your optimised molecule in it
• first check the summary, does your optimisation have D_3h symmetry?
• If your optimised molecule has D_3h symmetry save a "yourname_bh3_frequency.gjf" file from this logfile, close the logfile.
• If your optimised molecule does not have D_3h symmetry then you need to carry out an additional step to produce a D_3h symmetry log file.
  • From the main menu along the top of the screen (in gaussview) choose "file" and then "save" from the pull-down menu
  • a new window will open, with file names in it, save the file we have just opened file as "yourname_bh3_symmetry_opt.gjf" in the directory you created at the beginning of the lab. Don't forget the underscore, and make sure there are no spaces in the file name.
  • click on the save button
  • now we need to impose the symmetry, as you have done this before, the instructions will not be as detailed as previously. Go to the "edit" tab, select "Point Group ..." a new window will appear, tick "enable point group symmetry", choose constrain to subgroup D_3h. If D_3h does not appear on the menu click symmetrize, D_3h will then appear as an option, and you can select it. Now choose very tight for the tolerance and click OK.
  • We only constrain the symmetry for highly symmetric molecules and then only in certain situations, it is always best to work in C₁ (ie no symmetry) and then impose symmetry later if needed. Thus it is always important to check the symmetry of your molecule
  • run the job on your laptop or computer, it should complete very quickly. Open the log file and confirm from the summary that you have D_3h symmetry.
  • save a "yourname_bh3_frequency.gjf" file from this logfile, close the logfile.
• Now everyone should have a D_3h *.com file from which we can run a frequency calculation.

Edit the file to request a frequency analysis

• From the main menu along the top of the screen (in gaussview) choose "Calculation" and then choose "Gaussian":
• the calculation palette will appear. It opens with the "job type" tab open, now use the pull down menu under "energy" or "optmisation" to choose "frequency" (ignore the other stuff that appears)
• then click on the "title" tab to open it, and type "BH3 frequency"
• Then press submit (button is in the bottom left of the palette)
• a new window will pop-up and telling you that you must save the file first, press "save"
• a new window will then pop-up and ask you for a file name, it should already have the filename in the text area: "yourname_bh3_freq", and you should be in the folder you created at the start of the lab, if all this is true then press "save"
• a new window will then pop-up and ask you if you want to overwrite the file, and click yes. Then submit the job, press submit!
• close the molecule window, this is important as the "finished" molecule will look very similar to your starting one and many students accidentally take the wrong molecule!
• Wait for the message "Gaussian Job Completed ...", and click yes for opening a results file.

Investigating the frequency analysis job

• first we need to check that you have carried out the frequency analysis on the right file.
  • Open the "Summary" and check that the energy is the same as that recorded for your optimisation (it can vary in the last 2 decimal places but not any higher!), if the energies are different then you have different structures and you need to start this section again.
  • If you try this twice and it doesn't work ask a demonstator to help you (you will be doing something incorrectly and they will help you identify what it is).
• Now we are ready to look at the real output for this file
• select the results tab and "view file"
• scroll down until you find the following bit:

Low frequencies ---   -0.9033  -0.7346  -0.0056  6.7352  12.2482  12.2814
Low frequencies --- 1163.0004 1213.1854 1213.1881
Diagonal vibrational polarizability:
       0.7181241       0.7180239       1.8413645
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
                     1                      2                      3
                    A2"                    E'                     E'
Frequencies --  1163.0004              1213.1854              1213.1881
Red. masses --     1.2531                 1.1072                 1.1072
Frc consts  --     0.9986                 0.9601                 0.9601
IR Inten    --    92.5479                14.0553                14.0589
Atom  AN      X      Y      Z        X      Y      Z        X      Y      Z
    1   5     0.00   0.00   0.16     0.00   0.10   0.00    -0.10   0.00   0.00
    2   1     0.00   0.00  -0.57     0.00   0.08   0.00     0.81   0.00   0.00
    3   1     0.00   0.00  -0.57    -0.39  -0.59   0.00     0.14   0.39   0.00
    4   1     0.00   0.00  -0.57     0.39  -0.59   0.00     0.14  -0.39   0.00

• one important section is the two lines labeled "Low frequencies"
  • you know that every molecule has 3N-6 vibrational frequencies, the frequencies listed are these "-6"
  • these are just the motions of the center of mass of the molecule
  • these frequencies should be much smaller than the first vibration listed, for example the first vibration has A₂" symmetry and has a frequency of 1163cm^-1, the largest "zero" frequency is about 12cm^-1 which is an order of magnitude smaller ... so this looks ok.
  • The better the method employed the closer to zero these six frequencies should be.
  • We normally require these to be within plus/minus 15cm^-1. If your frequencies are not within this range you need to discuss this with a demonstrator.
  • For EVERY molecule you undertake a frequency analysis of you should include a cut-and-paste of the two "Low frequencies" lines. All of my research students are required to reproduce these lines in their workbooks.
• The next section in the output presents information related to the "real" frequencies of the molecule.
  • If you do not have the correct symmetry labels then your molecule does not have D_3h symmtery.
  • What you should have is frequencies close to mine, they may not be exactly the same due to slight differences in the optimisation, but they should be the same up to 1 cm^-1.
  • in the next section we are going to animate at the vibrations themselves and look at the computed "spectrum" generated from the data you are looking at now. The graphical interface will read this part of the file and will animate these frequencies for you.

Update your wiki

• Link to your completed 6-31G(d,p) BH₃ frequency file on your wiki
• Include the "summary" table in your wiki
• Include the low frequencies lines in your wiki
• Here is an example of my progressing wiki page.

When you are ready move onto the next step