JSpecView as a JCAMP-DX Data Viewer for Windows

History

In 1988, the Department purchased a diskless Perkin Elmer 1605 FTIR. To help in the process of being able to store the IR spectra recorded, two Pascal programs were written. The first to capture the files via the serial port (RS-232) and the second to display the data.

For information on the first program, FTtoPC, and other DOS utilities to convert files obtained from various instruments to JCAMP-DX format, see our JCAMP-DX utility page.

The original display program was totally rewritten in C++ and the code licensed to MDL in 1998 for incorporation into their plugin CHIME. Our contract with MDL has now finished (November 2005) but we will endeavour to be involved with future upgrades to the CHIME plugin. The last release (2.6 SP6) was April 2004 and this is available from the MDL web site..

In March 2006 we released JSpecView as an Open Source project at Sourceforge. A report on this is published in Chemistry Central Journal 2007, 1:31 (07Dec2007). The JAVA applet and application along with source code is being developed with JAVA 1.5+.

In some of the demonstrations and examples we show the use of links between spectra and molecular graphics display such that clicking on peaks in a Mass Spectrum will highlight the relevant FRAGMENTS in the molecule, clicking on peaks in the IR spectrum will highlight the relevant BONDS or animate the vibrational mode and clicking on peaks in the NMR will highlight the appropriate protons or carbon atoms. See below for more details on how to set up these links.

Justification

Information needed to configure a server for use with MDL CHIME

Joint Committee on Atomic and Molecular Physical Data Exchange References.

• JCAMP-CS vs 3.7 Ref.: Applied Spectroscopy, 1991, 45, 4.
• JCAMP-DX vs 4.24 for IR Ref.: Pure & Applied Chemistry, 1991, 63, 1781-92.
• for NMR vs 5.0 Ref.: Applied Spectroscopy, 1993, 47, 1093-1099.
• for MS vs 5.0 Ref. : Applied Spectroscopy, 1994, 48, 1545-1552.
• extension 5.01 for NMR, Ref.: Pure & Applied Chemistry, Vol. 71, No. 8, pp. 1549-1556, 1999.
• for IMS vs 5.01 Ref.: Pure & Applied Chemistry, Vol 73, No. 11, pp 1765-1782, 2001
• for NMR pulse sequences Ref.: Pure & Applied Chemistry, Vol 73, No. 11, pp 1749-1764, 2001
• for EMR vs 5.01 Ref.: Pure & Applied Chemistry,78(03), 613-631, 2006
• JCAMP-DX vs 5.01 with CD Ref.: Pure & Applied Chemistry, Vol 84, No. 10, pp. 2171�2182, 2012.

For an historical account of JCAMP-DX development, see the summary posted on the bionet.structure-nmr news group in January 1996. A local copy has been made available by the author.

The pages on JCAMP-DX by Antony Davies and Bob McDonald are essential reading for anyone interested in learning more about the JCAMP-DX specifications.
(Tony chairs the IUPAC working group on JCAMP-DX and Bob, who was a member, coauthored the original paper describing JCAMP-DX for IR). Both have provided test data for downloading from their web sites.

The method of encoding data, relies on substitution of numbers by ASCII characters. The following gives the compression tables used for this purpose.

Creating links between spectra and 3D molecular graphics display

//edit the following lines with caution!

var IRinfo = new Array();
function IRLinks(x,y,w,script,desc) {
  var n=IRinfo.length;
	IRinfo[n] = new Array();
	IRinfo[n].xpos=x;
	IRinfo[n].ypos=y;
	IRinfo[n].width=w;
	IRinfo[n].script=script;
	IRinfo[n].desc=desc;
}

var HNMRinfo=new Array()
function HNMRLinks(x,y,w,script){
 var n=HNMRinfo.length;
 HNMRinfo[n]=new Array();
 HNMRinfo[n].xpos=x;
 HNMRinfo[n].ypos=y;
 HNMRinfo[n].width=w;
 HNMRinfo[n].script=script;
}

var CNMRinfo=new Array();
function CNMRLinks(x,y,w,script){
 var n=CNMRinfo.length;
 CNMRinfo[n]=new Array();
 CNMRinfo[n].xpos=x;
 CNMRinfo[n].ypos=y;
 CNMRinfo[n].width=w;
 CNMRinfo[n].script=script;
}

//you should not need to edit the html files.

//edit the following lines with the spectral information

var IRfilName= "acetophenone.jdx";
var MolfilName= "acetophenone.xyz";

IRLinks(3101, 1, 20, 1,"symm stretch of aromatic CH group (~3100 cm-1)");
IRLinks(3086, 1, 15, 2,"asymm stretch of aromatic CH group (~3085 cm-1)");
IRLinks(3062, 1, 15, 3,"asymm stretch of CH group (~3060 cm-1)");
IRLinks(3038, 1, 10, 4,"asymm stretch of CH group (~3040 cm-1)");
IRLinks(3029, 1, 10, 5,"asymm bend of CH3 group (~3030 cm-1)");
IRLinks(3005, 1, 20, 6,"symm stretch of methyl group (~3005 cm-1)");
IRLinks(2969, 1, 30, 7,"asymm stretch of methyl group (~2970 cm-1)");
IRLinks(2921, 1, 30, 8,"symm stretch of CH group (~2920 cm-1)");
IRLinks(1684, 1, 30, 9,"Carbonyl stretching band (~1685 cm-1)");
IRLinks(1599, 1, 30, 12,"C-C of aromatic group (~1600 cm-1)");
IRLinks(1449, 1, 20, 14,"symm stretch of CH3 group (~1450 cm-1)");
IRLinks(1359, 1, 30, 16,"C-H twist of methyl group (~1360 cm-1)");
IRLinks(1265, 1, 20, 21,"scissors of aromatic C-H groups (~1265 cm-1)");
IRLinks(1180, 1, 40, 22,"scissors of CH group (~1180 cm-1)");
IRLinks(1078, 1, 30, 25,"symm stretch of CH3 group (~1080 cm-1)");
IRLinks(1025, 1, 20, 26,"symm stretch of CH group (~1025 cm-1)");
IRLinks(1001, 1, 20, 27,"asymm bend of CH3 group (~1000 cm-1)");
IRLinks(956, 1, 20, 28,"aromatic ring perturbation mode (~955 cm-1)");
IRLinks(760, 1, 20, 31,"aromatic ring perturbation mode (~760 cm-1)");
IRLinks(691, 1, 20, 33,"aromatic ring perturbation mode (~690 cm-1)");
IRLinks(588, 1, 20, 37,"concerted rocking mode of CH groups (~590 cm-1)");

var ShowDesc= "T";

var title= "acetophenone";
var author= "Prof. Robert John Lancashire";
var address1= "Department of Chemistry";
var address2= "University of the West Indies";
var address3= "Mona, Kingston 7, JAMAICA";
var lastMod= "8th March 2006";

//you should not need to edit the html files.

JSpecView (2006) and merged with Jmol 2012

JSmol - from 2013

Sample test files for error checking

Their product, GRAMS, uses .SPC binary files and a number of sites offer spectra in this format. Thermo offer a SPC Developers Kit for programmers to create their own file converters etc. Try their searchable database of IR and Raman spectra.

The following links may be useful for more details of databases and viewers:

• GRAMS/AI from Thermo Galactic Industries.
• JCAMP-DX software originally provided by Waters/Creon/LabControl
• JDXView and JDX2JDX free software and SOURCE CODE from Norbert Haider at the Univ of Vienna.
• The Spectroscopy Ninja by Friedrich Menges for interface to instruments and viewing spectroscopic data
• ShowSPC and IR files from the US EPA.
• Acorn NMR software (NUTS), this can import and export JCAMP-DX files.
• NMR files in NUTS format at Pacific Lutheran University.
• Widener NMR MS and FTIR resources
• Mestre-Lab software
• Chemistry WebBook database at NIST

ACD/Spectral Processing Software allows the user to process a range of spectral types: NMR, MS, UV, Visible, IR, NIR and Raman spectra. Supported file formats include the following: ACD (*.esp), Galactic (*.spc), JCAMP-DX (*.jdx, *.dx. *.jxs,*.jx) and ASCII (*.txt).

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