Using Chemistry properly on the Internet/Intranet

57. Using Chemistry properly on the Internet/Intranet

Antony N. Davies1 and Robert J.Lancashire2

1 ISAS, Inst. für Spektrochemie und Angewandte Spektroskopie, Bunsen-Kirchhoff-Str.11, 44139 Dortmund, Germany

2 Department of Chemistry, University of the West Indies, Mona, Kingston 7, Jamaica

Introduction
The reporting of scientific advances has basically not changed since the arrival of the printing press made scribes redundant. Finally we have – in the Internet Journal of Vibrational Spectroscopy – a medium to report our scientific advances by showing our science. We can now display in a scientific report our spectra as spectra and our chemical structures as chemical structures not just as pictures.

58. Chemical MIME
To enable this the Internet required an agreed protocol defining data types that are likely to be encountered. Agreed protocols are called Multipurpose Internet Mail Extensions (MIME) and have to be agreed by the Internet Engineering Task Force (IETF). Well recognised types are TEXT, IMAGE, AUDIO, VIDEO. For Chemistry the draft definitions are called Chemical MIME and have been pioneered by Henry Rzepa of Imperial College, London, UK and his colleagues. A table of some of the chemical MIME types is given in table 1. The latest information can be found at the following URL: http://www.ch.ic.ac.uk/chemime/

 

Primary/sub-type Suggested qualifier(s)
chemical/cxf cxf
chemical/mif mif
chemical/pdb pdb
chemical/cif cif
chemical/mdl-molfile mol
chemical/mdl-sdf sdf
chemical/mdl-rdf rdf
chemical/mdl-rxn rxn
chemical/embl-dl-nucleotide emb, embl
chemical/genbank gen
chemical/ncbi-asn1 asn
chemical/gcg8-sequence gcg
chemical/daylight-smiles smi
chemical/rosdal ros
chemical/macromodel-input mmd, mmod
chemical/mopac-input mop
chemical/gaussian-input gau
chemical/jcamp-dx dx, jdx
chemical/kinemage kin

59. Table 1

What this basically means is that any internet aware software should recognise a file called mydata.gau as a gaussian input file. Of more relevance for this article, a file called myspectrum.dx should be recognised as a JCAMP-DX spectrum and treated as such.

60. The JCAMP-DX MIME type for spectra display
So, having agreed on using the JCAMP-DX format for your spectrum on the Internet what is needed is a viewer which can display the spectrum as something more useful than a line of text! This has been made possible by the work of Robert Lancashire and co-workers who have written a utility which runs either as a stand-alone spectrum viewer or as an integrated part of your Web software as a plug-in for say Netscape. This is freely available and can be downloaded from http://wwwchem.uwimona.edu.jm:1104/software/jcampdx.html .

If you wish to run the the software as a plug-in, the file (npjdx.dll) must be located in the program\plugins subdirectory of your browser. You can check that the plug-in has been installed correctly by using the “About Plug-ins” menu from the Help menu item.

The next step is to try out your spectrum-enabled browser. You can do this by looking at some of the data available at http://wwwchem.uwimona.edu.jm:1104/spectra/index.html

61. If the plug-in is correctly installed (copied to the correct directory) you should see something like:

62. Alternatively look for some of the test data we have on our site here at ISAS: http://www.isas-dortmund.de/projects/lisms/biorad/difdup.dx which should show up as:

If you are not running a 32 bit system, then you should install the external viewer (jcampvw.exe). Select General Preferences and then Helpers.You can then use the Browse feature to locate the program which you have downloaded from Jamaica.

Finally, test the implementation on your own data by either writing a Web page with a link to one of your own JCAMP-DX files or by simply using the OPEN FILE command within your browser.

63. Chemical Structures
To activate your browser for chemical structures there are a number of plug-in’s available. One is MDL’s CHIME package available at http://www.mdli.com/chemscape/chime/.

With this installed you can produce great internet chemically active reports such as the ‘molecule-of-the-month’ pages. Try http://www.bris.ac.uk/Depts/Chemistry/MOTM/motm.htm for some good examples.

64. Support and Development
The JCAMP-DX standard has been adopted by IUPAC [1,2] and has a wide spread implementation amongst the spectrometer manufacturers. Following several meetings with the IUPAC Databases Committee it was decided that, in order to avoid competing development work on the same standard, an agreement should be drawn up between the JCAMP executive and IUPAC. This agreement committed the IUPAC Committee on Printed and Electronic Publications (CPEP) to set up a Working Party to support and develop the JCAMP-DX range of standards in return for financial support from the JCAMP organisation.

The working party has been very lucky in recruiting many of the people who have been developing the use of JCAMP-DX data standards world-wide.

Bob McDonald, an author of the first JCAMP-DX standard for infrared spectroscopy [3] had been pushing the adoption of these standards and publishing test data sets. He has also developed the use of the Internet for information on the JCAMP-DX standards with a very extensive reference site at http://members.aol.com/rmcdjcamp/index.htm.

65. In the European Community the standard had been adopted for food research within the Quest ‘Quality Established through Spectroscopic Techniques’ project. Here a lot of work was put in by Peter McIntyre of the University of Glamorgan, UK and Doug Rutledge of the Institut National Agronomique in Paris, France. An extended and unified version of the standard for food research was written and an extensive software suite developed to support this use.

The largest spectroscopic database project in recent years, the German government ‘Informationssystem Spektroskopie’ adopted the JCAMP-DX standards. It was used for data exchange between various project partners as well as for downloading data from the on-line version of the ‘SpecInfo’ databases available over STN International. During this project the next two Standards were published, JCAMP-DX for Nuclear Magnetic Resonance spectroscopy in 1993 [4] and JCAMP-DX for Mass Spectrometry in 1994 [5]. Both protocols were co-authored by Tony Davies, who is chairman of the IUPAC Working Party and Peter Lampen, who now works for the Deutsche Forschunganstalt für Lüft- und Raumfahrt in Berlin, Germany.

JCAMP-DX is one of the Chemical MIME types defined within Chemical MIME. Henry is not a member of this working party but is also leading a parallel working party on Chemical MIME reporting to the CPEP. Robert Lancashire of the University of the West Indies (UWI), Mona, Jamaica started using the JCAMP-DX standards as the most reliable method of moving spectroscopic data from his spectrometer for storage and into other applications such as spreadsheets. This interest developed into writing Windows programs to handle and display spectra via the JCAMP-DX standards. His group is now very active producing plug-ins and helper applications as well as Java scripts for JCAMP-DX standards to run with commercial Internet browser packages. This allows scientists to place spectroscopic data in the IUPAC recommended format on the Internet where it can be handled as spectra and not as purely graphical data.

66. Conclusions
Now we have the tools to produce a truly ‘active’ journal for vibrational spectroscopy on the internet. So I hope from now on all the spectra will be submitted as spectra and not as graphics or ‘high resolution’ PDF files !!! On this note the CLIC group have recently produced the first “enhanced” Chem Comm article [6] which includes a JCAMP-DX file of an infrared spectrum.

67. References

1. JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form (Recommendations 1991), Pure Appl. Chem. 63, 1781-1792 (1991)

2. Guidelines on Solution Nuclear Magnetic Resonance in Computerized Databases, C. Wilkins. Pure Appl. Chem. 67, 593-596 (1995)

3. JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form, Robert S. McDonald and Paul A. Wilks, Applied Spectroscopy 42 (1988) 151-162.

4. JCAMP-DX for NMR, Antony N. Davies and Peter Lampen, Applied Spectroscopy 47 (1993) 1093-1099.

5. JCAMP-DX for Mass Spectrometry, Peter Lampen, Heinrich Hillig, Antony N. Davies and Michael Linscheid, Applied Spectroscopy 48 (1994) 1545-1552.

6. A tetranickel(II) macrocyclic complex incorporating five different bridging groups, Paul E. Kruger and Vickie McKee, http://chemistry.rsc.org/rsc/c02788_1.htm

REF: Int. J. Vib. Spect., [www.irdg.org/ijvs] 1, 4, 57-67 (1997)