Molecular Vibrations

In order to predict equilibrium stable-isotope fractionations, it is necessary to know the characteristic frequencies of molecular vibrations.  It is also necessary to know how much each vibrational frequency in a molecule changes when a heavy isotope is substituted for a light one.  Vibrational frequencies for isotopically substituted molecules are not always known, so it is often necessary to use some type of force-field model to predict them.  Molecular vibrations are also important in understanding infrared absorption and the mechanisms and kinetics of chemical reactions.  Frequencies are most commonly measured with infrared or Raman spectroscopy.  Rotational-vibrational spectroscopy, isotope substitution, and many forms of force-field modeling are used to determine characteristic atomic motions.  This page shows some results from quantum-mechanical force-field modeling.

Transition elements like iron are most commonly found in octahedral and tetrahedral coordination environments.  Linear, trigonal-bipyramidal, square-planar, and cubic coordination also occur.  The links below show typical vibrational motions for molecules with some of these geometries.  Most of the animations show electronically neutral, gas phase molecules with the highest possible symmetry. The animations should reasonably approximate vibrational motions of complexes that are less symmetric or otherwise complicated because they are charged, in solution or part of a weak crystal lattice. Vibrational motions were calculated by normal-coordinate analysis with the ab initio electronic structure packages GAMESS and Gaussian03. Joseph Ochterski has written a good tutorial explaining in detail how an ab initio software package (in this case, Gaussian 03) calculates vibrational frequencies and motions.

Tetrahedral

CF4_tetrahedral
CF4, [FeCl4]-, CH4, CHClF2, CCl2F2 or CCl3F 

Octahedral

SF6_octahedral
SF6 or [Cr(H2O)6]3+

Linear

Square-planar

AuCl4-_square-planar
[AuCl4]-

Trigonal-bipyramidal

PF5_trigonal-bipyramidal
PF5

Pentagonal-bipyramidal

ReF7 Structure

Quicktime movies of the molecular vibrations were created with MacMolPlt. The Quicktime movies were converted to animated GIFs using GIFbuilder 1.0 and GraphicConverter 4.0.7. Vibrations in Hg(CH3)2 and ReF7 are animated using the Java applet Jmol. It may be necessary to update your computer's Java installation before viewing the Jmol animations.

Other GIFs of molecular vibrations:
    HF and HCl , from an example calculation predicting stable isotope fractionations using vibrational spectra.
    CO2
    H2O 
    N2O
    SO3
    NH3 
    CH4
    CHClF2
    CCl2F2
    CCl3F
    CCl2FCClF2
    The symmetric Fe-O stretch of [FeIII(H2O)6]3+ in solution.  This is a stereo image (cross your eyes to see the 3D effect).