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This paper was developed as part of Spring 2006
CONFCHEM
Web-Based Applications for Chemical Education: Experiences and
Visions
Return to the Spring'06
CONFCHEM |
Developing spectroscopic representations on the web.
Prof Robert John Lancashire
Department of Chemistry,
University of the West Indies,
Mona Campus, Kingston 7, JAMAICA
Email robert.lancashire@uwimona.edu.jm
Introduction.
In 1997, a group at UWI began collaboration with
MDL Information Systems Ltd and incorporated our spectroscopy
(JCAMP-DX) viewer code into MDL Chime. By 2005, when the contract
ended, MDL had clocked up over 2 million downloads of the free
version of the browser plug-in. MDL have stated that they will
continue to maintain Chime for at least another year but no
further updates to the spectroscopy viewer code are envisaged.
In March 2006, we followed up with the release of JSpecView
(http://jspecview.sourceforge.net),
an Open Source JAVA based spectroscopy viewer, which can be run
as an applet from a web page or as a standalone application to
display spectra encoded as JCAMP-DX or AnIML files.
There are several expected uses of JSpecView, and in this
presentation I will demonstrate examples where the applet can be
used in a teaching environment for the interpretation of IR, MS
and NMR spectra, delivery of spectral unknowns and in a
laboratory setting in combination with Jmol and another JAVA
applet for characterisation of visible spectra with Tanabe-Sugano
diagrams.
Some background to JCAMP-DX and AnIML
The Joint Committee on Atomic and
Molecular Physical Data (JCAMP) published their first data
exchange protocol in the 1980's. Since then the protocols for a
range of techniques have been developed and from 1995 IUPAC took
over the responsibility through the Committee for Printed and
Electronic Publications (CPEP). The types of spectra that are
commonly represented by JCAMP-DX file formats include: IR,
UV/Vis, MS (including GC/MS), NMR (with pulse sequence schemes),
IMS and EMR. By following these protocols it is possible to
generate files from other spectral techniques not already
covered, thereby extending this range.
The XML in Chemistry initiative within IUPAC started with a one
day meeting at the IUPAC General Assembly held in Brisbane in
2001. This was followed up by a consultation exercise to all
Divisions and then an open meeting in Cambridge 2002 for all
those who had expressed an interest.
The Analytical Information Markup
Language (AnIML) is a standardization effort of ASTM
(formerly the American Society for Testing and Materials)
Subcommittee E13.15 on Analytical Data, in conjunction with a
number of other groups including IUPAC.
AnIML provides an XML-based format for analytical data and is
designed specifically for spectroscopic and chromatographic data,
but once again is suitable for use with many different analytical
measurement techniques.
JSpecView - an Open Source project
The JSpecView Project provides an applet and application for the
display of JCAMP-DX and AnIML spectral files. For this
presentation I will be solely concentrating on the use of the
JAVA applet for web-based displays and leave discussion of the
application to another session!
The impetus for much of this has been that the web site I
maintain at the Department of Chemistry, UWI,
Mona has relied heavily on MDL Chime and has hundreds of
spectroscopic data files linked through its thousands of pages
that feature not only our coursework but the Chemistry of "Things
Jamaican" like our bauxite, rum, coffee and spices.
To get a feel for aspects of the site, check out the following
pages that are used in the interpretation and display of spectra.
In creating each of the these, the method employed was to
establish a template such that the necessary infrastructure to
display one set of information could be reused for the next set
without major recoding of HTML. This was achieved by storing
filenames and links etc. as small JavaScript files.
To be able to view the following pages requires that you have
a recent version of the Sun JRE installed (1.5 at least)
In the first example, the major peaks in the IR spectrum of
hexane are linked to animations of the vibrational modes which
are displayed using Jmol. Similar displays have been designed for
using Marvin and Chime.
In the display of the H NMR of aspirin, links are possible in
either direction. That is, it is possible to click on a peak in
the spectrum to highlight the H atom(s) or click on an H atom and
highlight the peak in the NMR.
For the Mass Spectrum example, the display initially shows the
molecule and the MS of dodecane. Using routines designed by
Professor Hanson, it is possible to predict a fragmentation list
from likely bond cleavages. Clicking on any of these links then
highlights the molecule in green and red to show the position of
bond cleavage and highlights that molecular ion in the spectrum.
Again this is bi-directional since clicking on a peak in the MS
will show the red/green molecular display as well.
The next example shows acetophenone as either an FTIR, H NMR or C
NMR spectrum. Initially the JCAMP-DX BLOCK file containing the 3
spectra is loaded and the different spectra are selected using a
radio button. With each display feedback to and from the Jmol
display is possible.
The last of these examples shows a simulated GC trace of pimento
oil (allspice). This has been an area of study in the Department
for many years and two of our Postgraduates have shown their
entrepreneurial skills by establishing a production facility in
the country for the export of pimento oil and eugenol.
Clicking on a peak in the GC shows the molecular graphic for that
component along with its MS.
Delivery of spectra for Organic unknowns
Traditionally, advanced organic laboratory programmes will have a
session where students are presented with unknown materials and
are asked to prepare derivatives and collect spectra to identify
the materials. In our course each student is issued with a solid
and a liquid and in the past were given a hard copy printout of
an IR and NMR spectra.
With time we have been able to build up a database of 150-200 IR,
UV/Vis, H NMR, C NMR, MS as well as some NIR spectra. For a
couple of years we used a web page form to deliver spectra using
MDL Chime, but due to problems with printing and the lack of an
Integration option for the NMR spectra the staff opted to return
to hard copies last year. I am determined to show that with
JSpecView incorporating functions for Integration and printing
that the on-line method provides advantages to the students who
can then access the information outside of laboratory hours so
that it will return to an on-line system in the near future.
Inorganic Laboratory experiment on Cr(III) complexes
In a previous Conf. Chem. series (1999b) I presented a paper on
the use of Tanabe-Sugano diagrams for the interpretation of
visible spectra of transition metal complexes.
Since then I have further developed the series of JAVA applets
for the display of TS diagrams and created a web page that
combines the d3 diagram appropriate for octahedral
Cr(III) complexes with the visible spectrum displayed in
JSpecView.
By selecting the peaks in the visible region the ratio of the
energies of these peaks is calculated and can then be used as
input to the TS diagram which returns the predicted position of
all the spin-allowed and forbidden transitions as well as the
Racah parameter, B.
spectra of Cr(III) complexes.
Conclusion
With a little effort it is possible to create web pages that can
display a wide range of spectral types and design teaching
material to support discussion of spectral interpretation.
In a laboratory setting, the ability to deliver live spectra that
can be manipulated, expanded, peaks highlighted etc. and printed
adds considerable value compared to hard copies.
Combining laboratory time with computer laboratory time allows
spectra to be recorded in one lab and interpreted in the other.
The overall impact, based on many favourable student responses is
that topics that are considered difficult can be simplified by
personal involvement rather than just trying to read and hear
about it.
Useful Electronic Resources
Confchem
presentation by Scott van Bramer on tools for processing and
interpreting spectral data.
SDBS:
Integrated Spectral Data Base System (bitmaps - not live
data)
Polymer Science Learning
Center with 200+ spectra
WebBook from NIST a source
for IR and MS JCAMP-DX files.
Jmol an Open Source JAVA
molecular graphics viewer.
Marvin from Chemaxon
another molecular graphics viewer (free for academic use)
MDL Chime browser plugin for
spectra and molecular graphics (free for academic use)
xvibs for generation of
vibrational mode xyz files
Babel
converter between molecular graphics formats
WebMO front end for
computational chemistry packages
MOPAC general-purpose semi-empirical molecular orbital
package
Copyright © 2006 by Robert John Lancashire, all rights
reserved.
