IR animations using JSpecView with JCAMP-DX FTIR files and jmol

This began as an idea for the NERMMW June 1998 workshop and the original examples were based on MDL Chime. 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 these issues was published in J. Chem. Educ., 2000, 77, 649.

The release of the Java applet JSpecView as an alternate JCAMP-DX viewer to MDL CHIME required that a separate molecular graphics viewer be used to view web pages featuring spectra and molecular graphics and showing the links between the two.

jmol is a Java applet that reads molecular graphics files such as MOL, PDB or XYZ format and Gaussian files and displays the animations for the vibrational modes. It is freely available from sourceforge and xvibs is now incorporated into it.

The steps involved in hotlinking the IR spectrum to show the vibrational mode origin of the peaks are:

1) Decide on a suitable molecule.
2) Draw it and save the coordinates.
3) Use any of the popular molecular modelling packages such as:
SPARTAN, MOPAC, HYPERCHEM or GAUSSIAN to perform a vibrational analysis calculation.
4) Using the output from this package 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, prepare the XYZ files showing the predicted fundamental vibrations.

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

5) record or obtain a copy of the IR spectrum in JCAMP-DX format.
6) use the IRauthoring tool to create the JavaScript file needed to render the links between the spectra and molecular display.

The link information is stored in JavaScript files and there is NO editing of the JCAMP-DX file.

7) save the file and edit the template (IRviewer.html) to include your new JavaScript file.
8) test your handiwork with the IRViewing template tool.

Clicking on a (major) peak in the IR should cause an animation file to be loaded showing that vibrational mode.

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

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

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

Return to IR pages or JSpecView pages, including NMR, MS and combinations.

Copyright © 2005 by Robert John Lancashire, all rights reserved.

Created and maintained by Prof. Robert J. Lancashire,
The Department of Chemistry, University of the West Indies,
Mona Campus, Kingston 7, Jamaica.
Created May 2005. Links checked and/or last modified 15th May 2005.