Differentiating M+ and M+H+ ions in an ESI+ MS experiment

In electrospray ionization MS (ESI-MS), ions are produced by the addition of a proton ([M+H]+). However, in cases where the analyte molecule is already charged, e.g. quaternary amine salts, the resulting ion may be an M+ ion.

Two ESI+ mass spectra are shown below. To test whether the molecular ion is M+ or M+H+, deuterium is added to the sample and the data is recollected. If the ion peak does not change in position relative to the original MS, the ion peak is considered an M+ and not M+H+.

Note: the deuterium exchange test may also occur with OH/NH/SH groups too. It is best to have a fair idea of the structure prior to performing this test.

Differentiating M+ and M+H+ ions in an ESI+ MS experiment

In electrospray ionization MS (ESI-MS), ions are produced by the addition of a proton ([M+H]+). However, in cases where the analyte molecule is already charged, e.g. quaternary amine salts, the resulting ion may be an M+ ion.

Two ESI+ mass spectra are shown below. To test whether the molecular ion is M+ or M+H+, deuterium is added to the sample and the data is recollected. If the ion peak does not change in position relative to the original MS, the ion peak is considered an M+ and not M+H+.

Note: the deuterium exchange test may also occur with OH/NH/SH groups too. It is best to have a fair idea of the structure prior to performing this test.

Elucidating for Isomers

The underlying essence of a structure elucidation process is to structurally distinguish an unknown from a set of possible isomers. This is evident by the number of possible isomers for a given molecular formula.

The chart below divides isomers into two groups: Structural/Constitutional/Regio and Stereo/Spatial isomers. Wikipedia links are included for further reading into the different isomer classifications.

 
  
Structural/Constitutional/Regio

Skeletal/Chain

Position

Tautomer

Isotopomers

Functional Groups

Stereo/Spatial

Diastereomers

Enantiomers

Cis/Trans

E/Z

Confomers

Rotamers

D/L

(+)/(-)

R/S

Epimers

Anomers

α/β

Elucidating for Isomers

The underlying essence of a structure elucidation process is to structurally distinguish an unknown from a set of possible isomers. This is evident by the number of possible isomers for a given molecular formula.

The chart below divides isomers into two groups: Structural/Constitutional/Regio and Stereo/Spatial isomers. Wikipedia links are included for further reading into the different isomer classifications.

 
  
Structural/Constitutional/Regio

Skeletal/Chain

Position

Tautomer

Isotopomers

Functional Groups

Stereo/Spatial

Diastereomers

Enantiomers

Cis/Trans

E/Z

Confomers

Rotamers

D/L

(+)/(-)

R/S

Epimers

Anomers

α/β

Advantages to a Broad and Focused Approach to Analyzing Data … Part 2

The previous blog described two general approaches to analyzing data for an unknown compound: broad and focused approaches.

The table below lists the general advantages of broad and focused approaches for a structure elucidation. Depending on the data at hand, one approach can be considered the better choice. An elucidation where lots of background information is available about the unknown favors the focused approach. A broad approach is best reserved for an elucidation where little is known about the unknown. This is a common issue for the elucidation of a natural product.

Advantages to a Broad and Focused Approach to Analyzing Data … Part 2

The previous blog described two general approaches to analyzing data for an unknown compound: broad and focused approaches.

The table below lists the general advantages of broad and focused approaches for a structure elucidation. Depending on the data at hand, one approach can be considered the better choice. An elucidation where lots of background information is available about the unknown favors the focused approach. A broad approach is best reserved for an elucidation where little is known about the unknown. This is a common issue for the elucidation of a natural product.

Approaches to Handling Data for an Unknown Compound

There are 2 general approaches to handling data for an unknown compound.

A. Start from a broad standpoint and work to narrow down the result(s). An example of this approach is to treat uncertain correlations on an HMBC as 4J coupling rather than as 3J coupling.

or

B. Start at a focused point and work outwards. An example of this approach is to begin with a specific core fragment and try to fit various substituents.

The bull’s eye diagram below offers a visual to the two approaches available to an elucidator. The answer, marked by the green X, can be reached by converging or diverging from the initial approach to the problem.