Tuesday, August 25, 2009

Determining the Site of Modification … Part 1

In past blogs, I have ascribed the process of peak matching as an integral part of structure elucidation. In this series, peak matching is demonstrated with the use of MS data.


The scheme below shows a parent compound (2-oxo-N,2-diphenylacetamide) with two possible sites for hydrogenation. The potential modified compounds are 2-hydroxy-N,2-diphenylacetamide and 2-hydroxy-1-phenyl-2-(phenylamino)ethanone labeled A and B, respectively.


MS3CompareToAPI_Scheme_Aug252009


The ESI+ full scan MS below belong to the parent compound (top) and the modified compound (bottom). With the given data, can the suspected site of modification be determined?


MS2CompareToAPI_Part1MS1_Aug252009  



Determining the Site of Modification … Part 1

In past blogs, I have ascribed the process of peak matching as an integral part of structure elucidation. In this series, peak matching is demonstrated with the use of MS data.


The scheme below shows a parent compound (2-oxo-N,2-diphenylacetamide) with two possible sites for hydrogenation. The potential modified compounds are 2-hydroxy-N,2-diphenylacetamide and 2-hydroxy-1-phenyl-2-(phenylamino)ethanone labeled A and B, respectively.


MS3CompareToAPI_Scheme_Aug252009


The ESI+ full scan MS below belong to the parent compound (top) and the modified compound (bottom). With the given data, can the suspected site of modification be determined?


MS2CompareToAPI_Part1MS1_Aug252009  



Tuesday, August 18, 2009

Using Peak Deconvolution to Extract the 1H Count

When you work on enough NMR datasets, eventually you will run into cases where peaks are overlapping. One approach is to apply a peak deconvolution (or fitting) algorithm in an attempt to separate out the contribution of each overlapping peak.


The 1H NMR spectrum below shows a multiplet (dd) nearly buried by a large water peak at 3.30 ppm.


DeconvolutionAnd1HCount_1_Aug182009


Direct integration of the multiplet will give a skewed value due to the contribution from the water peak. If the multiplet at 2.87 ppm equates to 1 proton, then how many protons does the multiplet at 3.24 ppm equate to?


The calculation is shown below:


1. Total RA = Relative Area(Water) + Relative Area(dd)


= 134.85 + 13.98 + 13.54 = 162.37


2. Total DA = Deconvoluted Area(Water) + Deconvoluted Area(dd)


= 30077 + 403 = 30480


3. (Deconvoluted Area(dd) / Total DA) = (Relative Area(dd) / Total RA)


  Relative Area(dd) = 403 * 162.37 / 30480 = 2.14 ~ 2 protons


DeconvolutionAnd1HCount_2_Aug182009


 



Using Peak Deconvolution to Extract the 1H Count

When you work on enough NMR datasets, eventually you will run into cases where peaks are overlapping. One approach is to apply a peak deconvolution (or fitting) algorithm in an attempt to separate out the contribution of each overlapping peak.


The 1H NMR spectrum below shows a multiplet (dd) nearly buried by a large water peak at 3.30 ppm.


DeconvolutionAnd1HCount_1_Aug182009


Direct integration of the multiplet will give a skewed value due to the contribution from the water peak. If the multiplet at 2.87 ppm equates to 1 proton, then how many protons does the multiplet at 3.24 ppm equate to?


The calculation is shown below:


1. Total RA = Relative Area(Water) + Relative Area(dd)


= 134.85 + 13.98 + 13.54 = 162.37


2. Total DA = Deconvoluted Area(Water) + Deconvoluted Area(dd)


= 30077 + 403 = 30480


3. (Deconvoluted Area(dd) / Total DA) = (Relative Area(dd) / Total RA)


  Relative Area(dd) = 403 * 162.37 / 30480 = 2.14 ~ 2 protons


DeconvolutionAnd1HCount_2_Aug182009




Wednesday, August 12, 2009

Distinguishing Impurities … Conclusion


In the blog series entitled Distinguishing Impurities, several types of NMR experiments were outlined to offer some insight into what to be on the look out for. Although there is no set guideline in this process, the best advice I may offer is to keep track of all the solvents, be aware of the possibility for sample degradation or side products, and finally if a signal does not look right, trial and error may be the only safe bet to ensure nothing is overlooked.


Below is a summary of the each part in the series:


Part 1 covered the aspects a 1H NMR whereby 2 singlets seemed out of place in relation to the remaining 1H signals.


Part 2 described some prep work to check for differences in the integrals of the 1H signals.


Part 3 depicted a 1H-13C HSQC with no obvious indicators that any of the 1H signals were impurities.


Part 4 illustrated how a 1H-1H DQF COSY was a bad choice when dealing with 1H singlets.


Part 5 had a 1H-1H TOCSY spectrum lacking any long range correlations with the 1H singlets.


Part 6 explained how the 1H-13C HMBC lacked any correlation trails with the 1H singlets.



Distinguishing Impurities … Conclusion


In the blog series entitled Distinguishing Impurities, several types of NMR experiments were outlined to offer some insight into what to be on the look out for. Although there is no set guideline in this process, the best advice I may offer is to keep track of all the solvents, be aware of the possibility for sample degradation or side products, and finally if a signal does not look right, trial and error may be the only safe bet to ensure nothing is overlooked.


Below is a summary of the each part in the series:


Part 1 covered the aspects a 1H NMR whereby 2 singlets seemed out of place in relation to the remaining 1H signals.


Part 2 described some prep work to check for differences in the integrals of the 1H signals.


Part 3 depicted a 1H-13C HSQC with no obvious indicators that any of the 1H signals were impurities.


Part 4 illustrated how a 1H-1H DQF COSY was a bad choice when dealing with 1H singlets.


Part 5 had a 1H-1H TOCSY spectrum lacking any long range correlations with the 1H singlets.


Part 6 explained how the 1H-13C HMBC lacked any correlation trails with the 1H singlets.



Monday, August 3, 2009

Blog on Hiatus from August 3 to 7

Due to some business travel, the blog P2C2E will be on hiatus for the week of August 3 to 7. Posts will resume next week.


For those unaware of the types of Bunsen burners available, below are the images for two types.


HiatusFor1Week_Aug42009



Blog on Hiatus from August 3 to 7

Due to some business travel, the blog P2C2E will be on hiatus for the week of August 3 to 7. Posts will resume next week.


For those unaware of the types of Bunsen burners available, below are the images for two types.


HiatusFor1Week_Aug42009