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Assembling a set of Fragments to Complete a Candidate Structure

October 1, 2008

The progression of a structure elucidation process is to examine the experimental data, compare the results to literature if possible, build a set of fragments based on the available data and finally assemble the fragments until a candidate structure(s) is reached. The assembly part is very much like working on a jigsaw puzzle. When all the pieces are present, it is as easy as matching up the right pieces by examining the overlap and/or trying out different combinations.

The following fragments #1-5 represent all the available information extracted from a set of experimental data. The letter A represents an open point of attachment.


The goal of the elucidator is to sort out what pieces belong together and which do not. Although more than one answer is possible, a candidate structure, 6-{[5-(trifluoromethyl)cyclopenta-1,4-dien-1-yl]methyl}-2,3-dihydropyridin-4(1H)-one, is colour-coded to illustrate how the fragments fit together to complete the structure.



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