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
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:
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 set of animations showing Mass Spectrum fragmentation using CHIME 2+ has been developed as well.
Copyright © 2004 by Robert John Lancashire, all rights reserved.Created and maintained by Prof. Robert J. Lancashire,