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)
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.
Clicking on a (major) peak in the IR should cause an animation file to be loaded showing that vibrational mode.
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.
Copyright © 2005 by Robert John Lancashire, all rights reserved.Created and maintained by Prof. Robert J. Lancashire,