Verifying, Confirming, Making Sure ... Part 1

After a long and arduous attempt at an elucidation, it is quite common to be left with more than one candidate structure. In some cases collecting more data is not an option and an exhaustive database/literature search turns up nothing useful, the alternative approach is to synthesize the proposed candidates and then compare the spectral data to the original unknown.

The example below shows three proposed candidate structure differing in the attachment of the hexopyranoside group. The high degree of similarity between the candidates and the high number of quaternary carbons (11 per structure) makes it very difficult to narrow the list to one candidate.

When data is limited and thus cannot assist in eliminating two out of the three candidates, then the only option left is to synthesize the candidates and compare the spectral data.  

Verifying, Confirming, Making Sure ... Part 1

After a long and arduous attempt at an elucidation, it is quite common to be left with more than one candidate structure. In some cases collecting more data is not an option and an exhaustive database/literature search turns up nothing useful, the alternative approach is to synthesize the proposed candidates and then compare the spectral data to the original unknown.

The example below shows three proposed candidate structure differing in the attachment of the hexopyranoside group. The high degree of similarity between the candidates and the high number of quaternary carbons (11 per structure) makes it very difficult to narrow the list to one candidate.

When data is limited and thus cannot assist in eliminating two out of the three candidates, then the only option left is to synthesize the candidates and compare the spectral data.  

Using a Smaller Structure to Elucidate a Larger Structure

Datasets for large unknown compounds tend to be complicated and typically require a lot of effort in distinguishing one signal from another. Having some background information about the unknown, such as a metabolite, a precursor, a derivative, etc. can be invaluable with the detail work needed to get through an elucidation.

The 13C NMR spectrum below is for an unknown compound with 38 carbons. Several carbons in the spectrum are overlapping with each other, thus, making the interpretation difficult.

To facilitate the process of elucidating the unknown, the 13C NMR spectrum for the unknown (drawn in black) is compared to the 13C NMR spectrum for a pure sample of cholesterol (drawn in red). The signals that line up are part of the same cholesterol scaffold; in all ~25 signals match up. The remaining 13 signals belong to the unknown part that requires further work.

 

The structures for the unknown and cholesterol are shown below.

Using a Smaller Structure to Elucidate a Larger Structure

Datasets for large unknown compounds tend to be complicated and typically require a lot of effort in distinguishing one signal from another. Having some background information about the unknown, such as a metabolite, a precursor, a derivative, etc. can be invaluable with the detail work needed to get through an elucidation.

The 13C NMR spectrum below is for an unknown compound with 38 carbons. Several carbons in the spectrum are overlapping with each other, thus, making the interpretation difficult.

To facilitate the process of elucidating the unknown, the 13C NMR spectrum for the unknown (drawn in black) is compared to the 13C NMR spectrum for a pure sample of cholesterol (drawn in red). The signals that line up are part of the same cholesterol scaffold; in all ~25 signals match up. The remaining 13 signals belong to the unknown part that requires further work.

 

The structures for the unknown and cholesterol are shown below.

Re-evaluating the data from MS and NMR … Part 4

With any type of data, there is an inherent risk of misinterpretation. My advice to elucidators is to consider multiple solutions and examine each one thoroughly. In the end, the answer to any problem set lies in tying together the bits of information in hopes of understanding the bigger picture.

Recap of the problem: The ESI+ MS shows a single [M+H]+ at m/z 102 allowing a maximum carbon count of 8. The 13C NMR shows there to be 12 carbons. How can the data from the MS and NMR present such different results for the same unknown?

The data from both the 13C NMR and DEPT-135 spectra are consistent with a mixture of two similar compounds at approximately a 1:1 ratio.

A mixture with an ESI+ MS exhibiting a single molecular ion indicates that the compounds in the mixture differ by a proton. For example, the mixture comprises of one compound with an R-NH2 group and the other with an R-NH3+ group. Some example amine/aminium mixtures are shown below.

Re-evaluating the data from MS and NMR … Part 4

With any type of data, there is an inherent risk of misinterpretation. My advice to elucidators is to consider multiple solutions and examine each one thoroughly. In the end, the answer to any problem set lies in tying together the bits of information in hopes of understanding the bigger picture.

Recap of the problem: The ESI+ MS shows a single [M+H]+ at m/z 102 allowing a maximum carbon count of 8. The 13C NMR shows there to be 12 carbons. How can the data from the MS and NMR present such different results for the same unknown?

The data from both the 13C NMR and DEPT-135 spectra are consistent with a mixture of two similar compounds at approximately a 1:1 ratio.

A mixture with an ESI+ MS exhibiting a single molecular ion indicates that the compounds in the mixture differ by a proton. For example, the mixture comprises of one compound with an R-NH2 group and the other with an R-NH3+ group. Some example amine/aminium mixtures are shown below.

Re-evaluating the data from MS and NMR … Part 3

Pattern recognition is an integral part of the process of structure elucidation. The quicker the elucidator can pick up on the pattern, the faster the elucidation can be accomplished and the less time wasted in elucidating the unknown.

Recap of the problem: The ESI+ MS shows a single [M+H]+ at m/z 102 allowing a maximum carbon count of 8. The 13C NMR shows there to be 12 carbons. How can the data from the MS and NMR present such different results for the same unknown?

The 13C NMR below shows a unique pattern that is not obvious at first. Each 13C signal seems to be paired to a nearby signal of similar peak intensity. The pattern is also noticeable in the 13C DEPT-135 NMR spectrum below.

 

This pairing pattern indicates that the unknown is a mixture at approximately a 1:1 ratio (note: the option of rotamers is also possible but is not being considered for this example). Therefore, instead of 12 carbons for a single unknown compound as perceived earlier, there are 6 carbons per unknown. This interpretation falls in line with what is being suggested by the MS data.

The last piece of the puzzle is to determine why the MS data shows only one molecular ion peak?