Making the connection between molecular structure and spectroscopy:
Jmol, JSpecView, and JCAMP-MOL
Robert M. Hanson, Robert Lancashire, and Amanda Leone
244th National Meeting of the American Chemical SocietyPhiladelphia, Pennsylvania
August 21, 2012
My Goals Today
• Briefly present JSpecView and its capabilities.
• Show how we have integrated JSpecView into Jmol.
• Discuss the extended JCAMP format we call JCAMP-MOL
JSpecView
• Open-source Java applet
• Reads a variety of data types, including– 1D and 2D NMR– IR and Raman– UV/VIS– GC, MS and GC/MS– Anything in JCAMP-DX format
http://jspecview.sourceforge.net
JSpecView
• Open-source Java applet
• Reads a variety of data types
• Recently integrated into Jmol
http://jspecview.sourceforge.net
NMR at St. Olaf College
http://chemapps.stolaf.edu/nmr/viewspec2
JSpecView – 2D NMR
http://chemapps.stolaf.edu/nmr/viewspec2
JSpecView – spectral comparison
http://chemapps.stolaf.edu/nmr/viewspec2
JSpecView – spectral overlay
http://chemapps.stolaf.edu/nmr/viewspec2
JSpecView – GC/MS
http://wwwchem.uwimona.edu.jm/spectra/JSpecView2
Jmol/JSpecView – integration
Jmol/JSpecView – peak selection
http://chemapps.stolaf.edu/nmr/viewspec2
Jmol/JSpecView – printing to PDF or laser printer
Jmol/JSpecView signed applets showing UV/Vis of Cr(III) spectra
Jmol/JSpecView applets – IR and Raman and symmetry
JCAMP-DX
• Introduced for IR in the late 1980s.
• Extended to a wide variety of data types.
• Specs at www.jcamp-dx.org
http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf
##TITLE= Compound file, contains several data records##JCAMP-DX= 5.0##DATA TYPE= LINK##BLOCKS=4##ORIGIN= Department of Chemistry, UWI, JAMAICA##OWNER= public domain
JCAMP-MOL
http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf
JCAMP-MOL
• A Single JCAMP file
• Containing:– Molecular structures– Spectral data– Correlation information
• Two additional JCAMP records:– ##$MODELS– ##$PEAKS
http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf
JCAMP-MOL ##$MODELS
http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf
##CAS REGISTRY NO=98-86-2##MOLFORM=C 8 H 8 O##$MODELS=<Models><ModelData id="acetophenone" type="MOL">acetophenoneRLDSViewer 3D 0
17 17 0 0 0 0 0 0 0 0999 V2000 -1.6931 0.0078 0.0000 C 0 0 0 0 0 0 0 0 0 1
JCAMP-MOL ##$PEAKS
http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf
##$PEAKS=<Peaks type="IR" xUnitsExpected="1/cm" >
<PeakData id="1" title="asymm stretch of aromatic CH group (~3100 cm-1)" peakShape="broad" model="1.2" xMax="3121" xMin="3092" />
<PeakData id="2" title="symm stretch of aromatic CH group (~3085 cm-1)“ peakShape="broad" model="1.1" xMax="3091" xMin="3072" />
…
</Peaks>
JCAMP-MOL ##$PEAKS
http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf
##$PEAKS=<Peaks type="HNMR" xUnitsExpected="ppm" >
<PeakData id="1" title="methyl group ~2.6" peakShape="singlet" model="acetophenone" atoms="15,16,17" xMax="2.7" xMin="2.5" />
<PeakData id="2" title="meta H's ~7.4" peakShape="multiplet" model="acetophenone" atoms="10,11" xMax="7.5" xMin="7.3" />
…
</Peaks>
Jmol/JSpecView Applets showing GCMS of pimento
Jmol Application showing JSpecView as a tool – MS
Jmol Application showing JSpecView as a tool - IR
Selecting an annotated peak will load an IR vibrational mode display in Jmol
Jmol + JME + JSpecView
JCAMP-MOL
http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf
