Structural Elucidation An Example

A considerable number of NMR experiments have been introduced and discussed in this book. In order to illustrate how a series of such experiments is used in practice, we will take the reader through a complete structural elucidation of the compound T-2 toxin, many of whose 2D spectra were encountered in Chapter 7. If we had no knowledge of the compound s structure, our study would begin with the determination of its infrared, h NMR, 

and high-resolution mass spectra. T-2 toxin is a white solid that is soluble in chloroform. 

Strong infrared absorptions centered at 1,740 and 1,100-1,300 cm suggest the presence of two or more carbonyl groups, which more likely are ester functionalities than ketone groups. Moreover, the occurrence of 9 oxygens in the molecular formula supports the inference that the carbonyl absorptions are probably due to ester, rather than ketone, groups. 

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The chemical shift of a nucleus depends in part on its spatial position in relation to a bond or a bonding system. The knowledge of such anisotropic effects is useful in structure elucidation. An example of the anisotropic effect would be the fact that axial nuclei in cyclohexane almost always show smaller H shifts than equatorial nuclei on the same C atom (illustrated in the solutions to problems 37, 47, 48, 50 and 51). The y-effect also contributes to the corresponding behaviour of C nuclei (see Section 2.3.4). 

Some dihydropyran-2-ones are natural products and mass spectrometry has proved to be a useful tool in structure elucidation. For example, massoilactone (147), which is secreted by formicine ants, was characterized by its mass spectrum. On electron impact, the alkyl group is readily cleaved generating an ion at m/e 97 (68AJC2819). This process parallels the behaviour of other simple lactones. 

The X,"Y correlation techniques described so far do not allow to determine the number of magnetically equivalent detected "X nuclei. Such information is frequently of importance for structure elucidation for example, it would permit to determine the number of phosphine ligands in a metal complex from a P-detected phosphorus-metal shift correlation. A remedy to this problem has been found by recording fully coupled correlation spectra in which the number of X spins can be derived from the multiplet structure in FI. This is easily achieved in both HMQC and HSQC pulse schemes by omitting the refocusing 180° pulse during ti, and various correlations have been performed in this For an interpretation of the results,... 

Point-dipole approximation with delocalized electron spin This method is an extension of the point-dipole approximation, applicable to paramagnetic species with spin density distributed over several atoms. Hyperfine (hf) interactions in hydrogen-bonded systems and trapping site structure with surrounding ions can be elucidated. An example briefly discussed in Section 2.2.2 is the model deduced from ENDOR measurements on X-irradiated Li-formate for the trapping of CO2 ion radicals in a crystal matrix. The dipolar hfc is composed of contributions from spin densities at three atoms as indicated by the sketch to the right in Fig. 2,12. A procedure to add the contributions described in Appendix A2.1 involves the following steps. 

The determination of molecular formula in this way is enormously helpful for structure elucidation. For example, an unknown compound with a molecular formula of C3H6O cannot possibly be an amine (no nitrogen present), an ester or carboxylic acid (both requiring two oxygen atoms). In other words, the molecular formula, once determined, can be used to eliminate some structural types from consideration. 

In Summary Fragmentation patterns can be interpreted for structural elucidation. For example, the radical cations of alkanes cleave to form the most stable positively charged fragments, haloalkanes fragment by rupture of the carbon-halogen bond, alcohols readily dehydrate and undergo a cleavage, and alkenes break an allylic bond to form a resonance-stabilized carbocation. 

The early investigations of the reactions of the penicillin class of compounds were largely of a degradative nature, and were primarily associated with structure elucidation. These have been discussed in detail (B-49MI51102) and some of the principal transformations are outlined in Schemes 2, 3 and 4 using benzylpenicillin as an example. Some of these reactions will be discussed in greater detail later in this section. 

Chemical techniques for the isolation, purification and elucidation of the structure of toxins have evolved to the extent that it is frequently a routine procedure to identify the chemical nature of a newly discovered toxin once it has been purified, although difficulties arise when the toxin is a very large polypeptide, protein, or a very complex organic molecule. However, it is sometimes found that a toxin becomes progressively more labile and stabilizing contaminants are removed by the purification processes. An example of this is Cyanea toxic material which becomes increasingly labile with each purification step 111). 

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