Ah Sugar, Sugar … Residue

Sugar residues (saccharides) can be tough to elucidate. They tend to have 1H NMR spectrum with overlapping and sometimes poorly-resolved 1H signals, and the 2D NMR data presents lots of ambiguous assignments. With a little practice, an elucidator can quickly pick out a sugar moiety based on a minimal amount of NMR data.

For a given set of atoms with known 13C chemical shifts (shown below), a hexopyranoside sugar moiety is evident even without any long-range coupling information. The general pattern is as follows: a CH at ~100 ppm, 4 CHs between ~70 to 77 ppm, a CH2 at ~60 ppm, 6 O atoms and 4 H atoms. Note: the H atoms count may vary depending on the number of connection points.

An example sugar, phenyl hexapyranoside, with 13C chemical shifts is presented below.

Ah Sugar, Sugar … Residue

Sugar residues can be tough to elucidate. They tend to have 1H NMR spectrum with overlapping and sometimes poorly-resolved 1H signals, and the 2D NMR data presents lots of ambiguous assignments. With a little practice, an elucidator can quickly pick out a sugar moiety based on a minimal amount of NMR data.

For a given set of atoms with known 13C chemical shifts (shown below), a hexopyranoside sugar moiety is evident even without any long-range coupling information. The general pattern is as follows: a CH at ~100 ppm, 4 CHs between ~70 to 77 ppm, a CH2 at ~60 ppm, 6 O atoms and 4 H atoms. Note: the H atoms count may vary depending on the number of connection points.

An example sugar, phenyl hexapyranoside, with 13C chemical shifts is presented below.

Two years later and still elucidating

February 1, 2010 marked the second year anniversary of the weblog P2C2E. I would like to dedicate this milestone to you the loyal readers. Thank you.

According to Google Feedburner, the weblog has 36 email subscribers while averaging about 80-100 readers accessing it daily. The weblog carrier Typepad reports a total of 46,708 lifetime page views. With 128 posts, the weblog ranks within the top 4 hits in Google searches for the key words elucidation and structure elucidation. The site is linked on various websites such as: Chemspider Blog, NMR Wiki, Top 50 Biotech Blogs, Chemical blogspace, University of Ottawa NMR Facility Blog, Ryan’s Blog on NMR Software, Stan’s NMR Blog, Queen’s University Website, etc., etc., etc., etc.

Please note that due to some business travel followed by vacation time, the weblog will be on hiatus for 3 weeks from February 2 to 19.

 

Two years later and still elucidating

February 1, 2010 marked the second year anniversary of the weblog P2C2E. I would like to dedicate this milestone to you the loyal readers. Thank you.

According to Google Feedburner, the weblog has 36 email subscribers while averaging about 80-100 readers accessing it daily. The weblog carrier Typepad reports a total of 46,708 lifetime page views. With 128 posts, the weblog ranks within the top 4 hits in Google searches for the key words elucidation and structure elucidation. The site is linked on various websites such as: Chemspider Blog, NMR Wiki, Top 50 Biotech Blogs, Chemical blogspace, University of Ottawa NMR Facility Blog, Ryan’s Blog on NMR Software, Stan’s NMR Blog, Queen’s University Website, etc., etc., etc., etc.

Please note that due to some business travel followed by vacation time, the weblog will be on hiatus for 3 weeks from February 2 to 19.

 

Correlating 1D NMR data on an HMBC

There are many challenges present in deciphering correlations on an HMBC experiment. Barring any data collection issues, most of the challenges will arise from signals that are overlapping, thus, adding an element of ambiguity.   

The 1H -13C HMBC spectrum below shows a correlation between the 13C at 71.2 ppm and the overlapping 1H signals at 2.08 (d) and 2.12 (m) ppm. There is nothing usually here, right?

A nearby correlation on the same 1H -13C HMBC spectrum (see below) shows a correlation between the 13C at 75.01 ppm and the 1H at 2.28 ppm. The splitting pattern for this correlation suggests that the previous correlation might also be splitting. If this is the case, then the correlation is centered on 71.26 and 2.10 (m) ppm, and thus, there is no correlation to the doublet at 2.08 ppm. In the end, further analysis of the overlapping multiplets between 2.00-2.15 ppm is needed to resolve the ambiguity.

Correlating 1D NMR data on an HMBC

There are many challenges present in deciphering correlations on an HMBC experiment. Barring any data collection issues, most of the challenges will arise from signals that are overlapping, thus, adding an element of ambiguity.   

The 1H -13C HMBC spectrum below shows a correlation between the 13C at 71.2 ppm and the overlapping 1H signals at 2.08 (d) and 2.12 (m) ppm. There is nothing usually here, right?

A nearby correlation on the same 1H -13C HMBC spectrum (see below) shows a correlation between the 13C at 75.01 ppm and the 1H at 2.28 ppm. The splitting pattern for this correlation suggests that the previous correlation might also be splitting. If this is the case, then the correlation is centered on 71.26 and 2.10 (m) ppm, and thus, there is no correlation to the doublet at 2.08 ppm. In the end, further analysis of the overlapping multiplets between 2.00-2.15 ppm is needed to resolve the ambiguity.

Qualitative Elucidation via TLC Staining

TLC (Thin Layer Chromatography) offers a simple approach to identifying a solvent(s) for separating out a mixture, monitoring a reaction to completion, etc. Furthermore, the TLC plates can be stained to identify the presence or absence of various functional groups such as amines, ketones, etc. This qualitative experiment does offer various drawbacks.

The process of staining typically requires the items shown in the illustration below.

 The following websites offer more insight into the process of staining.

http://webpub.allegheny.edu/employee/s/smurphre/research/visualization.pdf

Org Prep Daily: http://orgprepdaily.wordpress.com/2006/09/27/tlc-staining-solutions/

Curly Arrow Blog: http://curlyarrow.blogspot.com/2006/11/lets-talk-about-tlcs-part-1-vanillin.html