Transcript Jmol Model Kit Mode

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 Society
Philadelphia, 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
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
Jmol/JSpecView – printing to PDF or laser printer
http://chemapps.stolaf.edu/nmr/viewspec2
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
##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
http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf
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 ##$MODELS
##CAS REGISTRY NO=98-86-2
##MOLFORM=C 8 H 8 O
##$MODELS=
<Models>
<ModelData id="acetophenone" type="MOL">
acetophenone
RLDSViewer
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
http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf
JCAMP-MOL ##$PEAKS
##$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>
http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf
JCAMP-MOL ##$PEAKS
##$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>
http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf
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