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Using complementary elucidation tools to solve for an unknown structure

June 30, 2008

MS and NMR are complementary tools for structure elucidation. Knowing when to apply which tool can assist an elucidator in solving for an unknown structure quickly and with less frustration. Although the sample data below is for a simple organic structure, it is working through many simple examples that one refines the skills needed for elucidation(s) on a bigger scale.

With the available spectral data below, the steps outlined for elucidating an unknown are as follows:

1. extract peak information from the spectral data,

2. piece together the fragments to build a complete structure,

3. finally, verify that the candidate structure(s) is consistent with all the spectral data. If more than one structure fits the data, then look into collecting additional data.

Below are three spectra for an unknown compound: an EI MS, a 1H NMR and a 13C NMR. Although additional information can be extracted from the spectral data, an explanation follows to some of the obvious bits of information that can be extracted at a first pass. The MS shows pairs of ion clusters at approximately equal intensity for m/z pairs 79/81, 93/95 and 133/135, thus indicating the presence of a bromine atom. The molecular ion is most likely the ion peak at m/z 133. The nitrogen rule indicates that the unknown contains an odd number of nitrogen atoms. The 1H NMR spectrum shows 2 triplets at a 1:1 ratio and coupled to each other. The 13C NMR shows 3 carbon peaks at 21, 24 and 117 ppm, thus indicating 3 carbon atoms.

Nmrms_june302008

The structural pieces are a bromine atom (79 Da), a nitrogen atom (14 Da), -CH2-CH2- group (28 Da) and a third carbon (12 Da). The candidate structure that fits the data is 3-bromopropanenitrile (133 Da).

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