Congratulations, and a big thank you, to all involved – this is great work.  The potential of the new “triad” for teaching and learning is clear, and exciting!  The underlying additions to the SMILES capabilities of Jmol sound very interesting and will offer new opportunities for development of interactive web pages.

 

Mike 

 

From: Robert Hanson [mailto:hansonr@stolaf.edu]
Sent: 01 February 2014 19:54
To: jmol-users@lists.sourceforge.net; Robert Lancashire
Subject: [Jmol-users] jmol-14.1.8_2014.02.01 -- Get your predicted NMR spectra here!

 

Robert Lancashire and I are happy to announce the first online open-source fully JavaScript fully customizable 1D HNMR prediction tool. Perfect for the classroom or for research laboratories, a demonstration showing how easy it is to set up a web page is available (http://chemapps.stolaf.edu/jmol/jsmol/jsv_predict2.htm). All that is required a few script tags and a bit of initialization code. Full JavaScript code is at
 
  http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.8_2014.02.01.zip

This update of Jmol fully integrates JSME, Jmol, and JSpecView into a JavaScript-only HTML5 triad that can be used on any page and in any combination on any platform to display and analyze predicted 1D 1HNMR spectra, allowing for comparison to actual spectra and to each other. Spectra can be displayed independently, overlaid, or set above one another in a synchronized set.

Either real or imagined compounds can be drawn quickly using JSME or loaded from NCI using a chemical name, InChI, InChI-Key, SMILES, or CAS#.

Peaks in the spectrum and atoms in either the 2D drawing or the the 3D structure can be selected, with corresponding atoms and peaks in the other applets automatically highlighting.

Spectra can be zoomed, panned, integrated, and saved as PDF files. Peaks and coupling constants can be measured.

The JSME/Jmol duo by itself allows for simple correlation between 2D drawings and 3D structures without reference to NMR spectra. In addition, the JSpecView JavaScript applet can independently display 1D and 2D NMR spectra originating as JCAMP-DX files locally or from a server as well as IR, Raman, UV/VIS, GC, GC/MS data in that same format or in AnIML XML format. (Note that JSpecView is currently being used as the front end for St. Olaf's fully robotic 400-MHz NMR (http://chemapps.stolaf.edu/nmr/)  JSpecView can also integrate with Jmol to display JCAMP-MOL (http://chemapps.stolaf.edu/jmol/docs/misc/Jmol-JSpecView-specs.pdf) files, which are used here for communication with EPFL.

Many thanks to Luc Patiny (EPFL), Peter Ertl (Novartis), and Bruno Bienfait (Molecular Networks)  for their assistance with this very challenging project. Supreme thanks to Markus Sitzmann for the NCI CACTVS chemical identifier resolver, which was key to this entire operation. Thanks also to Joćo Aires de Sousa for the neural-network NMR prediction algorithms and online service used to generate the NMR spectra.

New capabilities of Jmol originating from this project include the capability to generate SMILES codes indicating all H atoms explicitly, to easily compare models of the same compound from two different sources, such as PubChem and NCI, and to easily map atom numbers between different 2D and/or 3D mol files originating from different sources using different algorithms for their construction.

Bob Hanson
Robert Lancashire



--

Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900