IR animations

IR animations using JSpecView applet with JCAMP-DX FTIR files

A paper discussing many of the issues is available in J. Chem. Educ., 2000, 77, 649.

The JSpecView applet can display spectra while molecular graphics can be displayed with MDL Chime, Jmol and Marvin. To link between the two, it is possible to use JavaScripts, Rasmol or MDL Chime scripts 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 xvibs-17 (written in 1990 by Milan Hodoscek) and ported to JAVA and now maintained by Steven Wheeler, then a single XYZ file is produced showing all 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 limited 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 scripts written 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 JavaScript file. Clicking on a (major) peak in the IR should cause an animation frame in the XYZ file to be loaded showing that vibrational mode. Alternatively, use one of the following as a template and modify the JavaScript file with the link information appropriate for your compound.

Fully worked samples available so far include:

2-chloroaniline from MOPAC and using Jmol
3-chloroaniline from MOPAC and using Jmol
4-chloroaniline from MOPAC and using MDL Chime
4-chloroaniline from MOPAC and using Jmol
4-chloroaniline from MOPAC and using Marvin
acetophenone from MOPAC and using Jmol
adipic acid from MOPAC and using Jmol
cyclohexene from MOPAC and using Jmol
cyclohexanol from MOPAC and using Jmol
cyclohexanone from MOPAC and using Jmol
N-ethylaniline from MOPAC using Jmol
N,N-diethylaniline from MOPAC using Jmol
n-hexane from MOPAC using Jmol
phenol from MOPAC and using Jmol
phenyl benzoate from MOPAC using Jmol
vinylpyrrolidinone from MOPAC using Jmol
m-xylene from MOPAC using Jmol

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

Jmol like xvibs is Open Source and freely available from SourceForge. xvibs is now incorporated into Jmol.

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 and NMR links using JSpecView has been developed as well.

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

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

Created April 2005. Links checked and/or last modified 15th January 2008.
URL http://wwwchem.uwimona.edu.jm/spectra/JSpecView/iranim/index.html