Using more and molden to view a vibrational analysis

• Sign on to unix and have this web page open on the screen at the same time as your xterm window.  Remember, you must be using X windows (Exceed) for molden to work
• cd ~nbwt3/work/listen
• Use the standard unix program more to look at the file:

more cc6tbpm3frq.log
• This is the Gaussian output file for a vibrational analysis of twist-boat cyclohexane at the PM3 semiempirical level, which you have calculated in the  Exercise on modelling, using Arguslab
• Use / to scan for freq
• This shows the Gaussian command line.  This asks for a single-point rhf/pm3 run, reading the initial guess and the geometry from a checkpoint file (where a previous geometry optimisation run had stored them).  The keyword freq tells Gaussian to perform a vibrational analysis (i.e. calculate vibration frequencies)
• Note that a vibrational analysis must be done using the same method and basis set, as the geometry has been optimised at, otherwise the results are meaningless
• Use the more command n to search for the next occurrence of freq
• This takes you to the beginning of the vibrational analysis output
• Nine 'low frequencies' are listed (over two lines)
• The first three correspond to translations, and are shown as negative to indicate that they are imaginary
• The next three are about zero, and are rotations
• The final three are the lowest three vibrations, and are repeated in the big table which follows
• If there were any imaginary vibrations, the structure would be a saddle point:  the program would print a warning.  Here, all is well
• In the big table of vibrations
• The frequencies are in cm^-1, as measured in an IR or Raman spectrometer
• Relative IR intensities are given
• In this run, Raman activities were not calculated, but they can be if needed
• The x,y,z columns for each atom for each vibration, are a vector showing the amplitude of the movement of the atom:  e.g. in the vibration at 70.2517 cm^-1, none of the carbon atoms move in the x direction
• Notice that the vibration at 482.7872 cm^-1 has zero IR intensity:  why do you think this is?
• After the table of vibrations come the thermochemical results, of which the most useful for energy calculations are:
• Zero-point vibrational energy
• Thermal correction to Energy
• Sum of electronic and thermal Energies
• The thermal energies are calculated at 298.150 K, but a different temperature can be specified in setting up the calculation
• When you have finished looking at the .log file, exit from more with q

Using molden to animate the vibrations

• Give the BWT unix command molden
• In the molden control window, press the Read button
• You will see a listing of the directory from which you invoked molden
• Single click on the name of the log file cc6tbpm3frq.log
• Switch off the Molden File Select window by pressing its Close button
• Press Solid, Ball & Stick
• Switch off the hydrogens by pressing the H button, then Excl. All Hydrogens
• Click the black dot in the bottom right hand corner of the control window, to allow the structure to be rotated by left dragging
• Press Norm. Mode
• A Molden Frequency Select window will appear, in which the calculated vibration frequencies are listed
• Click on 482.7... and click on the molden molecule window:  the molecule should be executing the vibration
• Can you see now why this vibration has no IR intensity?
• Try turning the molecule so that you are looking along each of its 2-fold axes in turn, as you did in the Arguslab modelling drylab
• Turn on the hydrogens by pressing the H button again
• Try looking at some more of the vibrations, including the one at highest frequency
• How would you describe the highest frequency vibration?
• When you have finished with molden, press the skull and crossbones to exit
• When you have finished with unix, type exit