Making the connection between molecular structure and spectroscopy: Jmol, JSpecView, and JCAMP-MOL

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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
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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

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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
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JSpecView

• Open-source Java applet
• Reads a variety of data types
• Recently integrated into Jmol

http//jspecview.sourceforge.net
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NMR at St. Olaf College
http//chemapps.stolaf.edu/nmr
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NMR at St. Olaf College
http//chemapps.stolaf.edu/nmr/viewspec2
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JSpecView 2D NMR
http//chemapps.stolaf.edu/nmr/viewspec2
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JSpecView spectral comparison
http//chemapps.stolaf.edu/nmr/viewspec2
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JSpecView spectral overlay
http//chemapps.stolaf.edu/nmr/viewspec2
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JSpecView GC/MS
http//wwwchem.uwimona.edu.jm/spectra/JSpecView2
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Jmol/JSpecView integration
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Jmol/JSpecView peak selection
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Jmol/JSpecView printing to PDF or laser printer
http//chemapps.stolaf.edu/nmr/viewspec2
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Jmol/JSpecView signed applets showing UV/Vis of
Cr(III) spectra
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Jmol/JSpecView applets IR and Raman and symmetry
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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 BLOCKS4 ORIGIN Department of
Chemistry, UWI, JAMAICA OWNER public domain
http//chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSp
ecView-specs.pdf
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JCAMP-MOL
http//chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSp
ecView-specs.pdf
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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-JSp
ecView-specs.pdf
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JCAMP-MOL MODELS
CAS REGISTRY NO98-86-2 MOLFORMC 8 H 8
O MODELS ltModelsgt ltModelData
id"acetophenone" type"MOL"gt acetophenone RLDSVie
wer 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-JSp
ecView-specs.pdf
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JCAMP-MOL PEAKS
PEAKS ltPeaks type"IR" xUnitsExpected"1/cm"
gt ltPeakData id"1" title"asymm stretch of
aromatic CH group (3100 cm-1)"
peakShape"broad" model"1.2" xMax"3121"
xMin"3092" /gt ltPeakData id"2" title"symm
stretch of aromatic CH group (3085 cm-1)
peakShape"broad" model"1.1" xMax"3091"
xMin"3072" /gt lt/Peaksgt
http//chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSp
ecView-specs.pdf
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JCAMP-MOL PEAKS
PEAKS ltPeaks type"HNMR" xUnitsExpected"ppm"
gt ltPeakData id"1" title"methyl group 2.6"
peakShape"singlet"
model"acetophenone" atoms"15,16,17" xMax"2.7"
xMin"2.5" /gt ltPeakData id"2" title"meta
H's 7.4" peakShape"multiplet"
model"acetophenone" atoms"10,11" xMax"7.5"
xMin"7.3" /gt lt/Peaksgt
http//chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSp
ecView-specs.pdf
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Jmol/JSpecView Applets showing GCMS of pimento
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Jmol Application showing JSpecView as a tool MS
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Jmol Application showing JSpecView as a tool - IR
Selecting an annotated peak will load an IR
vibrational mode display in Jmol
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Jmol JME JSpecView
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JCAMP-MOL
http//chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSp
ecView-specs.pdf