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.

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.

Is the round-bottom flask half full or half empty?

Just as there are a variety of fishes in the sea, structure elucidators come in a variety of forms. What makes a qualified elucidator good? Yeah, luck and natural talent can play a role sometimes but it is not an exclusive club by any means. A good elucidator is typically ambitious with a wealth of experience and knowledge under his/her belt. A good elucidator uses a variety of tools and leaves no stone unturned. Not all elucidators need to have an optimistic outlook on a challenge, but definitely be persistent, through and through.

Typically, an unqualified elucidator will take random stabs at a problem without any real direction. Like an athlete preparing for a competition, practice makes perfect. Some up and coming elucidators will take longer to get good while others catch on faster. Over time and with lots of practice, an inexperienced elucidator can sharpen their skills and grow into an experienced and qualified elucidator.

Is the round-bottom flask half full or half empty?

Just as there are a variety of fishes in the sea, structure elucidators come in a variety of forms. What makes a qualified elucidator good? Yeah, luck and natural talent can play a role sometimes but it is not an exclusive club by any means. A good elucidator is typically ambitious with a wealth of experience and knowledge under his/her belt. A good elucidator uses a variety of tools and leaves no stone unturned. Not all elucidators need to have an optimistic outlook on a challenge, but definitely be persistent, through and through.

Typically, an unqualified elucidator will take random stabs at a problem without any real direction. Like an athlete preparing for a competition, practice makes perfect. Some up and coming elucidators will take longer to get good while others catch on faster. Over time and with lots of practice, an inexperienced elucidator can sharpen their skills and grow into an experienced and qualified elucidator.

How much is too much Apodization for an NMR FID?

For a structure elucidation process, applying an apodization (or window function) to an NMR spectrum can be a good thing and sometimes can be a bad thing. Making peaks broader can assist in differentiating signals from noise, but can also cause neighboring peaks to mesh into a single resonance. The best approach in handling spectral data is to consider an extra processing step and FT with minimal or no apodization.

The 13C NMR spectra below illustrates the effects of different numerical values for line broadening on two 13C resonances. At an exponential line broadening of 2 Hz, the two 13C resonances appear as a single resonance. The result is an underestimated carbon count. If no apodization is applied, the 2 carbon resonances are clearly visible.

TIP: FT an FID with and without line broadening and compare the results. This simple extra step can save loads of time when working on an elucidation problem.

How much is too much Apodization for an NMR FID?

For a structure elucidation process, applying an apodization (or window function) to an NMR spectrum can be a good thing and sometimes can be a bad thing. Making peaks broader can assist in differentiating signals from noise, but can also cause neighboring peaks to mesh into a single resonance. The best approach in handling spectral data is to consider an extra processing step and FT with minimal or no apodization.

The 13C NMR spectra below illustrates the effects of different numerical values for line broadening on two 13C resonances. At an exponential line broadening of 2 Hz, the two 13C resonances appear as a single resonance. The result is an underestimated carbon count. If no apodization is applied, the 2 carbon resonances are clearly visible.

TIP: FT an FID with and without line broadening and compare the results. This simple extra step can save loads of time when working on an elucidation problem.

How to reference 1D and 2D NMR spectra? … Part 3

Certain experimental conditions, such as varying the temperature or using different solvents, can influence the interpretation of NMR data. Although it can be useful to collect data with different solvents (e.g. DMSO-d6 or Chloroform-d) or temperatures to decrease peak overlap in a particular region, it can complicate the structure elucidation process by increasing the amount of spectral data at hand. When it comes to referencing 2D NMR data, use the 1D NMR data collected at the same temperature and solvent.

The 1H NMR spectra below are for the same compound quinine prepared with different deuterated solvents. The shifts in the peaks are a result of the different effects of the solute-to-solvent interactions. When analyzing 2D NMR data for an elucidation, be sure to use the 1D NMR with the same experimental conditions to ensure all peaks and correlations are aligned correctly.

TIP: the best data to work with is the one with the least amount of peak overlap.

How to reference 1D and 2D NMR spectra? … Part 3

Certain experimental conditions, such as varying the temperature or using different solvents, can influence the interpretation of NMR data. Although it can be useful to collect data with different solvents (e.g. DMSO-d6 or Chloroform-d) or temperatures to decrease peak overlap in a particular region, it can complicate the structure elucidation process by increasing the amount of spectral data at hand. When it comes to referencing 2D NMR data, use the 1D NMR data collected at the same temperature and solvent.

The 1H NMR spectra below are for the same compound quinine prepared with different deuterated solvents. The shifts in the peaks are a result of the different effects of the solute-to-solvent interactions. When analyzing 2D NMR data for an elucidation, be sure to use the 1D NMR with the same experimental conditions to ensure all peaks and correlations are aligned correctly.

TIP: the best data to work with is the one with the least amount of peak overlap.