Identification of Adduct Ions

Depending on sample preparation, adduct ions can be present on a mass spectrum. The goal of the elucidator is to identify whether an adduct ion(s) is present and its contribution to the mass (or elemental composition) of the unknown compound.

The example ESI+ mass spectrum below exhibits 2 ion clusters at m/z 951.305 and 973.287, corresponding to ions [M+H]+ and [M+Na]+ respectively. For this spectrum, sodiation is identified by taking the difference between the two masses at 21.982 g/mol and comparing it to the mass of a sodium ion at 22.989 g/mol minus the mass of a proton at 1.007 g/mol. The mass of the unknown at 950.298 g/mol is calculated by subtracting the contribution of the sodium adduct or the mass of a proton at 1.007 g/mol from the respective peak.

  

Identification of Adduct Ions

Depending on sample preparation, adduct ions can be present on a mass spectrum. The goal of the elucidator is to identify whether an adduct ion(s) is present and its contribution to the mass (or elemental composition) of the unknown compound.

The example ESI+ mass spectrum below exhibits 2 ion clusters at m/z 951.305 and 973.287, corresponding to ions [M+H]+ and [M+Na]+ respectively. For this spectrum, sodiation is identified by taking the difference between the two masses at 21.982 g/mol and comparing it to the mass of a sodium ion at 22.989 g/mol minus the mass of a proton at 1.007 g/mol. The mass of the unknown at 950.298 g/mol is calculated by subtracting the contribution of the sodium adduct or the mass of a proton at 1.007 g/mol from the respective peak.

  

Molecular Formula from a ‘Spot On’ Ion Peak

With a well-tuned and calibrated, high resolution MS instrument, a molecular formula(e) can be devised from the m/z for an ion peak. In cases where more than one molecular formula fits, knowing the accuracy of the MS instrument can help in narrowing down the choices.

The first step is to identify the molecular ion peak and its ionization, e.g. [M+H]+, [M+Na]+, etc. so as to take into account any additional adduct information in fitting a molecular formula. Secondly, use common elements with likely valences such as C, H, O, N (III, IV, V) and S (II, IV, VI) to try to fit a molecular formula.

An ESI+ mass spectrum for an unknown organic compound is shown below. The cationized peak at m/z 216.1749 corresponds to an [M+H]+ and is accurate up to four significant decimal places. The following table illustrates how a mass tolerance of 0.001 Da can assist in narrowing down the list of molecular formulae.

 

#     MF                 Mass (Da)     Difference

1 C15H21N1         215.1674         0.0003

2 C12H25N1S1      215.1708         0.0037

3 C10H21N3O2     215.1634         -0.0037

Molecular Formula from a ‘Spot On’ Ion Peak

With a well-tuned and calibrated, high resolution MS instrument, a molecular formula(e) can be devised from the m/z for an ion peak. In cases where more than one molecular formula fits, knowing the accuracy of the MS instrument can help in narrowing down the choices.

The first step is to identify the molecular ion peak and its ionization, e.g. [M+H]+, [M+Na]+, etc. so as to take into account any additional adduct information in fitting a molecular formula. Secondly, use common elements with likely valences such as C, H, O, N (III, IV, V) and S (II, IV, VI) to try to fit a molecular formula.

An ESI+ mass spectrum for an unknown organic compound is shown below. The cationized peak at m/z 216.1749 corresponds to an [M+H]+ and is accurate up to four significant decimal places. The following table illustrates how a mass tolerance of 0.001 Da can assist in narrowing down the list of molecular formulae.

 

#     MF                 Mass (Da)     Difference

1 C15H21N1         215.1674         0.0003

2 C12H25N1S1      215.1708         0.0037

3 C10H21N3O2     215.1634         -0.0037

Coincidental 13C peaks on an HMBC Spectrum

When interpreting data from a 1H-13C HMBC without a high-resolution 1D 13C NMR, there is the possibility to miss coincidental overlapping carbons. As such, always consider a missing carbon or two as part of the structure elucidation for an unknown.

The 1H-13C HMBC below—note the lack of a high-resolution 1D 13C NMR spectrum—exhibits a 2-3J correlation between a proton at 8.1 ppm (H1) and a carbon at 128 ppm (C2).

Using the fragment information below, a quick structural assumption is that the unknown contains a 5 membered ring. Another possibility is that 2 coincidental carbon peaks are overlapping at 128 ppm. As such, a 6 membered ring is also possible.

 

Coincidental 13C peaks on an HMBC Spectrum

When interpreting data from a 1H-13C HMBC without a high-resolution 1D 13C NMR, there is the possibility to miss coincidental overlapping carbons. As such, always consider a missing carbon or two as part of the structure elucidation for an unknown.

The 1H-13C HMBC below—note the lack of a high-resolution 1D 13C NMR spectrum—exhibits a 2-3J correlation between a proton at 8.1 ppm (H1) and a carbon at 128 ppm (C2).

Using the fragment information below, a quick structural assumption is that the unknown contains a 5 membered ring. Another possibility is that 2 coincidental carbon peaks are overlapping at 128 ppm. As such, a 6 membered ring is also possible.

 

The Facets of Structure Elucidation

I would like to begin the new year with a weblog that summarizes the components of an elucidation process. Each component, shown as a Venn diagram below, can blend in with the next until a conclusion is reached. The goal for the elucidator is to exhaust all aspects of each possible component thus ensuring that nothing is overlooked.

Collect/Process/Organize Data

Dereplication/Database/Library search

Peak matching

Fragment assembly

Verification

Publish/Report/Present/Store

   

The Facets of Structure Elucidation

I would like to begin the new year with a weblog that summarizes the components of an elucidation process. Each component, shown as a Venn diagram below, can blend in with the next until a conclusion is reached. The goal for the elucidator is to exhaust all aspects of each possible component thus ensuring that nothing is overlooked.

Collect/Process/Organize Data

Dereplication/Database/Library search

Peak matching

Fragment assembly

Verification

Publish/Report/Present/Store