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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. 244 th National Meeting of the American Chemical Society Philadelphia, Pennsylvania August 21, 2012. My Goals Today.

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

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  1. 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

  2. My Goals Today • Briefly present JSpecViewand its capabilities. • Show how we have integrated JSpecView into Jmol. • Discuss the extended JCAMP format we call JCAMP-MOL

  3. 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

  4. JSpecView • Open-source Java applet • Reads a variety of data types • Recently integrated into Jmol http://jspecview.sourceforge.net

  5. NMR at St. Olaf College http://chemapps.stolaf.edu/nmr

  6. NMR at St. Olaf College http://chemapps.stolaf.edu/nmr/viewspec2

  7. JSpecView – 2D NMR http://chemapps.stolaf.edu/nmr/viewspec2

  8. JSpecView – spectral comparison http://chemapps.stolaf.edu/nmr/viewspec2

  9. JSpecView – spectral overlay http://chemapps.stolaf.edu/nmr/viewspec2

  10. JSpecView – GC/MS http://wwwchem.uwimona.edu.jm/spectra/JSpecView2

  11. Jmol/JSpecView – integration

  12. Jmol/JSpecView – peak selection

  13. Jmol/JSpecView – printing to PDF or laser printer http://chemapps.stolaf.edu/nmr/viewspec2

  14. Jmol/JSpecView signed applets showing UV/Vis of Cr(III) spectra

  15. Jmol/JSpecView applets – IR and Raman and symmetry

  16. 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

  17. JCAMP-MOL http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf

  18. 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

  19. 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

  20. 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

  21. 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

  22. Jmol/JSpecView Applets showing GCMS of pimento

  23. Jmol Application showing JSpecView as a tool – MS

  24. Jmol Application showing JSpecView as a tool - IR Selecting an annotated peak will load an IR vibrational mode display in Jmol

  25. Jmol + JME + JSpecView

  26. JCAMP-MOL http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf

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