Verify Twice, Publish Once

The message behind an old carpenter’s adage ‘measure twice, cut once’ can be applied to the process of structure elucidation as ‘verify twice, publish once’. Committing the time to double check a candidate structure against the experimental data can save a lot of hassles and embarrassment from a mistake being published/presented/stored/reported. Without picking on a specific case, journals are littered with examples of incorrect structures.

As the holidays approach, Philosophy to Chemistry to Elucidation blogging will be taking a short break and will resume in the new year. In the meantime, the following link is an interesting read on the importance of shape within the field of Chemistry: Angew. Chem. Int. Ed. Engl. 30 (1991)1-16.

Verify Twice, Publish Once

The message behind an old carpenter’s adage ‘measure twice, cut once’ can be applied to the process of structure elucidation as ‘verify twice, publish once’. Committing the time to double check a candidate structure against the experimental data can save a lot of hassles and embarrassment from a mistake being published/presented/stored/reported. Without picking on a specific case, journals are littered with examples of incorrect structures.

As the holidays approach, Philosophy to Chemistry to Elucidation blogging will be taking a short break and will resume in the new year. In the meantime, the following link is an interesting read on the importance of shape within the field of Chemistry: Angew. Chem. Int. Ed. Engl. 30 (1991)1-16.

Missing the Big Picture?

When peak picking a 2D NMR experiment, past weblogs have advocated zooming in on correlations especially in cases dealing with ambiguity. Depending on the data collection parameters, a 1H-13C HMBC experiment can contain paired 1J coupling responses. Without careful scrutiny of the data, these extra responses can be misinterpreted as long-range correlations (2J or longer).

The 1H -13C HMBC spectrum below indicates two peaks picked, thus, correlating proton 1.24 ppm to carbon 20.47 ppm and proton 1.35 ppm to carbon 23.07 ppm. This is an easy interpretation that cannot possibly be wrong, or is it?

    

Before accepting the peak picking, it is best to take a step back—actually zoom out a little further to get the bigger picture. The correlations from the 1H -13C HMBC spectrum are 1J coupling responses and thus not long-range correlations. The blue lines indicate the paired 1J coupling responses. When assigning long-range correlations, 1J coupling responses are best not to be picked.

    

NOTE: Although it is possible for a long-range correlation to overlap with a 1J coupling response, it may be wise to examine the volumes of the responses for any significant differences.

Missing the Big Picture?

When peak picking a 2D NMR experiment, past weblogs have advocated zooming in on correlations especially in cases dealing with ambiguity. Depending on the data collection parameters, a 1H-13C HMBC experiment can contain paired 1J coupling responses. Without careful scrutiny of the data, these extra responses can be misinterpreted as long-range correlations (2J or longer).

The 1H -13C HMBC spectrum below indicates two peaks picked, thus, correlating proton 1.24 ppm to carbon 20.47 ppm and proton 1.35 ppm to carbon 23.07 ppm. This is an easy interpretation that cannot possibly be wrong, or is it?

    

Before accepting the peak picking, it is best to take a step back—actually zoom out a little further to get the bigger picture. The correlations from the 1H -13C HMBC spectrum are 1J coupling responses and thus not long-range correlations. The blue lines indicate the paired 1J coupling responses. When assigning long-range correlations, 1J coupling responses are best not to be picked.

    

NOTE: Although it is possible for a long-range correlation to overlap with a 1J coupling response, it may be wise to examine the volumes of the responses for any significant differences.

Confirmation of Synthesis: using MS to identify a protective group

Many organic chemists employ Mass spectrometry (MS) as a convenient verification tool for their product in a synthetic reaction. Derivatization such as adding a protective (or protecting) group can often be detected by MS.

The EI mass spectrum for tert-butyl 3-aminopiperidine-1-carboxylate is shown below. The 'terminal' atoms belonging to the protective group, tert-Butyloxycarbonyl (BOC or t-BOC), are coloured in blue. Although the parent ion is not clearly evident, the mass spectrum shows 3 ion clusters: m/z 57, 99 and 127 with the associated fragments listed below.

 

Confirmation of Synthesis: using MS to identify a protective group

Many organic chemists employ Mass spectrometry (MS) as a convenient verification tool for their product in a synthetic reaction. Derivatization such as adding a protective (or protecting) group can often be detected by MS.

The EI mass spectrum for tert-butyl 3-aminopiperidine-1-carboxylate is shown below. The 'terminal' atoms belonging to the protective group, tert-Butyloxycarbonyl (BOC or t-BOC), are coloured in blue. Although the parent ion is not clearly evident, the mass spectrum shows 3 ion clusters: m/z 57, 99 and 127 with the associated fragments listed below.