Vibrational modes using Gaussian
This exercise follows the drylab Geometry
optimisation using Gaussian and uses checkpoint files left in the unix
directory /usr/local/tmp1/n.. where n.. is your user id
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Make sure the files are still there by
dir /usr/local/tmp1/n..
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If one or more of your .chk files is not there, you will need to run its
geometry optimisation again, using the .com file which you should still
have stored in your own file space in work/g98
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Do this by
g98 filefirstname &
as in the previous drylab
Making a command file for Gaussian, to perform a vibrational analysis for
PCl5
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For this exercise, you should create Gaussian command files with names
like pcl5vib.com to distinguish them from e.g. pcl5.com which was for the
geometry optimisation
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From your work/g98 unix directory, using an xterm window for which you
have set
up the Curlew keyboard, start by
cp pcl5.com pcl5vib.com
cl !$
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You are now editing a copy of your .com file, called pcl5vib.com
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Using the arrow keys, move to the first line of your original Z matrix
(i.e. the line below the 0 1 line)
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Press control-b to set on the block marker
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Click Esc then h to go to the end of the file
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Move up until Curlew's cursor is on the last line of data
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Hold down the control key and tap u once
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This rubs out the entire Z matrix (in this copy) but leaves the two or
three blank lines at the bottom of the file
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The last visible line should now be the 0 1 line
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Now move to the Gaussian command line (starting with #P pm3) and along
to the beginning of the opt keyword
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Overwrite the opt keyword with the following
geom=check guess=check freq
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This tells Gaussian to read the last geometry from the checkpoint file
(whose name you have not changed at the top of the file), and to read the
starting guess from the checkpoint file, and then to do a vibrational analysis
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Save the file with Esc then x
Running Gaussian
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This is done in exactly the same way as for the geometry optimisation in
the previous drylab, using
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For these molecules at this level, this takes even less machine time than
the geometry optimisation did
Looking at the output
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As before, you can look at the .log file using Curlew
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You see 'Redundant internal coordinates taken from checkpointfile' and
then the table of 'Initial Parameters', which should be the same as the
optimised geometry at the end of the optimisation run
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Go on down until you find the 'Standard basis' line, as before
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This is now followed by 'Initial guess read from the checkpoint file'
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Gaussian now goes on to do a single point MO calculation, in which it also
calculates derivatives of the energy in order to obtain force constants
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Search for the word 'frequencies' by pressing function key F6 and entering
/freq/
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This is the beginning of a table of predicted vibrational frequencies,
with the relative movement of each of the atoms in the x, y and z directions,
for each
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Some of the vibrations have zero IR Intensity because they are symmetric
and do not change the dipole moment of the molecule
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Leave this window showing this part of the output, while you also look
at it using Molden
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Run Molden from a different xterm window looking at your work/g98 directory
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Read in pcl5vib.log and set the view to shaded
balls and sticks as before
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Turn the molecule so that the threefold axis is approximately vertical,
and you can see all three equatorial atoms clearly
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Click Norm. Mode and a Frequency Select dialog
box will appear
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Click the one of the pair of degenerate frequencies at about 604 cm-1
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This clearly changes the dipole moment and will be IR active
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Click on 401 cm-1
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The undistorted molecule has no dipole, and this vibration does not create
one, so it is not seen in the IR
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What about the vibration at 332 cm-1?
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The hard ones to work out are the pair at 195 cm-1: the
.log file says this is IR inactive, which you can confirm by looking up
the character table for D3h in the back of a textbook such as
Huheey: the vibration has E'' symmetry
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The point is that neither the axial bonds nor the equatorial plane are
changing their geometry, so neither is generating a change in dipole.
Only the angle between the 'axial' bonds and the equatorial plane is changing.
If you add a zero change in dipole to a zero change in dipole, you get
zero, whatever the angle
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When you have finished looking, stop the motion in Molden by clicking Norm.
Mode again: because Molden is running
in a distant computer, all the movement is being transmitted to your Exceed
server in real time over the network. A whole class of students doing
this at the same time could slow things up considerably for other users
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In your other xterm window, exit from Curlew with
Esc then z
[PCl6]- and [PCl4]+
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Repeat the procedure above to see the vibrations
of the two ions
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[PCl4]+ is so very nearly tetrahedral
that the vibrations appear the same as for a tetrahedron
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You should be able to remember some of the vibrations
for tetrahedral and octahedral molecules from your other courses