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     COLLOQUIUM OF THE COMPUTATIONAL MATERIALS SCIENCE CENTER
   AND THE SCHOOL OF PHYSICS, ASTRONOMY AND COMPUTATIONAL SCIENCES
                       (CSI 898-Sec 001)
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      A Roadmap for Systematic Data Representations in Cyberinfrastructure 
   for Combustion Research: Proposed Refinements of Unique Representations 
        for Identifying Molecular Entities in Chemical Kinetics 

                       Donald R. Burgess, Jr.
     National Institute of Standards and Technology, Gaithersburg, MD 

The IUPAC International Chemical Identifier (InChI) has been widely adopted and uses a 
canonical string to represent the structure of a molecule.  In essence, the atoms in a 
molecule and their connectivities are represented using the simplest possible unique 
numbering scheme.  An InChI string, however, cannot distinguish between some molecular 
entities that have the same structure, but substantially different chemical reactivities, 
nor can InChI strings provide unique representations of elementary chemical reactions 
(i.e., transition states  - which transform one molecule to another).  This limits the 
utility of InChI as a useful identifier for applications in chemical kinetics.

We propose the development additional layers for InChI that are able to uniquely
and  unambiguously identify different molecular entities including rotational
conformers, transition states, and radicals with different resonance structures. We also
propose that an additional reaction layer be developed to provide for a unique
representation of elementary reactions: InChI specifies which bonds exist in the molecule; 
the reaction layer would simply specify which bonds are being broken or formed during the
reaction.  Successful implementation of InChI formalism into the field of chemical
kinetics would be a powerful aid in providing systematic representations of sets of 
chemical reactions.

                     Monday, December 5, 2011
                               4:30 pm
                    Room 301, Research I, Fairfax Campus

Refreshments will be served at 4:15 PM.
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Find the schedule at http://cmasc.gmu.edu/seminar/schedule.html