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

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

http://jspecview.sourceforge.net/

JSpecView

• Open-source Java applet

• Reads a variety of data types

• Recently integrated into Jmol

http://jspecview.sourceforge.net

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



JSpecView – spectral comparison



JSpecView – spectral overlay



JSpecView – GC/MS

http://wwwchem.uwimona.edu.jm/spectra/JSpecView2

http://wwwchem.uwimona.edu.jm/spectra/JSpecView2/

Jmol/JSpecView – integration

Jmol/JSpecView – peak selection


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


JCAMP-MOL

• A Single JCAMP file

• Containing:– Molecular structures– Spectral data– Correlation information

• Two additional JCAMP records:– ##$MODELS– ##$PEAKS


JCAMP-MOL ##$MODELS


##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


##$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


##$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


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

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