Part 1: Boron Based Acids

E: Frequency Analysis and Confirming the Minimum

I hope you remember from your pre-university days that while the first derivative of a function tells us the slope, it doesn't tell us if we are at a maximum or a minimum point! For example consider the case where there is a barrier to dissociation in our one dimensional example, as shown below, both the maximum of the barrier (the transition state) and the minimum (the ground state) have a slope of zero.

We will have to take the second derivative, if the second derivative is positive we have a minimum and if the second derivative is negative we have a maximum. The second derivative gives the curvature of the function, how this works is shown in the figure below.

The frequency analysis is essentially the second derivative of the potential energy surface, if the frequencies are all positive then we have a minimum, if one of them is negative we have a transition state, and if any more are negative then we have failed to find a critical point and the optimisation has not completed or has failed. The frequency analysis has another important role to play because it provides the IR and Raman modes to compare with experiment.

• Now we are going to carry out a frequency analysis to confirm we have a minium structure. This MUST to be carried out on the fully optimised structure
• The first thing we need to do is to open the file from your bH₃ optimisation and to save a copy to work with (incase you make a mistake and need to start from the original file again).
  • 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
  • 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_freq.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
  • check the text across the top of the molecule window, it should have your new filename
• You now have a renamed copy of the original optimised molecule which we are now going to edit in order to carry out 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 click on the "link 0" tab to open it, and after "%chk=" type "yourname_bh3_freq", make sure you type the underscores as linux is sensitive to extra spaces, replace "yourname" with your first name ... remember NO extra spaces!! For example you might have "sally_bh3_freq"
• Finally in the text area headed "Additional key words" type "pop=full", this requests a full analysis of the electron density and MOs which we will need later. (Do not add any extra spaces!)
• 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 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.

  

• When you are ready move onto the next step which is animating the vibrations you have just calculated!