IR animations

IR animations using CHIME 2+ (WIN32 only) with JCAMP-DX FTIR files

This began as an idea for the NERMMW June 1998 workshop. For the follow-up meeting in January 1999, some guidelines and objectives were prepared for the use of these animations in teaching spectroscopy and the details for the method of preparation of simple web pages given. Further details coming from the workshop can be viewed at the U. Mass. (Amherst) Chemistry and Microbiology sites.
A paper discussing all the issues is available in J. Chem. Educ., 2000, 77, 649.

Since CHIME version 2+ can display both spectra and molecular graphics and link between the two, then why not use hyperlinks from the spectrum to show the origin of the peaks. Popular molecular modelling packages such as SPARTAN, MOPAC, HYPERCHEM and GAUSSIAN can perform vibrational analysis calculations.

Using their output and VIBREAD.EXE (written by Prof P. Lahti at U Mass), or xvibs (written in 1990 by Milan Hodoscek) and ported to JAVA and now maintained by Bradley A. Smith, then XYZ files were produced showing the predicted fundamental vibrations.

WebMO allows for on-line submission to Gaussian and within the 3 minute allowed time frame it is possible to do an analysis of small molecules.

A local copy of WebMO and MOPAC is located on an Intranet LINUX server. Access is to UWI, Mona staff and students only.

Note that the individual peak analysis gives the computed vibrational peak positions, which are typically overestimated by about 18-22%!

The experimental FTIR spectra were recorded and saved as JCAMP-DX files and header lines added to make the links between the spectrum and molecular graphic display. This process has been somewhat automated by using a set of authoring tools and the final display only requires the author to modify about 6 lines of a simple text file. Clicking on a (major) peak in the IR should cause an animation file to be loaded showing that vibrational mode.

Fully worked samples available so far include:

acetophenone from SPARTAN
p-xylene from SPARTAN
o-xylene from Gaussian 90
m-xylene from Gaussian 90
p-xylene from Gaussian 90
acetone from Gaussian 90
acetaldehyde from Gaussian 90
2-chloroaniline from Gaussian 90
3-chloroaniline from Gaussian 90
4-chloroaniline from Spartan
ethyl benzoate from MOPAC.

With the release of MDL CHIME SP4 it is now possible to use JavaScript functions to achieve similar results but without editing the JCAMP-DX file.
An example that can be used as a template to build further working vibtrational mode animations has been done for hexane.

Now test your ability to assign peaks on your own by trying cyclohexene and/or 1,3-dimethoxybenzene and/or n-octanol and/or paracetamol.

For some background on IR modes of vibration see the animations of the different types e.g. symmetric, asymmetric, scissors, etc.

A JAVA applet that reads molecular graphics files such as PDB format and Gaussian files and displays the animations for the vibrational modes has been developed by The OpenScience Group. jmol is freely available from them and xvibs is now incorporated into it.

For prediction of IR spectra on-line and the display of their normal modes of vibration using VRML, see ComSpec3D.

A set of animations showing Mass Spectrum fragmentation using CHIME 2+ has been developed as well.

Return to IR page or spectroscopy pages, including NMR, MS and UV-Vis.

Created and maintained by Prof. Robert J. Lancashire,
The Department of Chemistry, University of the West Indies,
Mona Campus, Kingston 7, Jamaica.

Created June 1998. Links checked and/or last modified 11th April 2004.
URL http://wwwchem.uwimona.edu.jm/spectra/iranim/index.html