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A biased elucidation is an elucidation where the chemist makes certain assumptions about the data at hand based on a previous experience(s) and not deviating from it. Depending on the elucidation, it can be a good thing or a very bad thing. As a good thing, it can speed up the time spent on an...

A calculated neutral loss spectrum is obtained from a mass spectrum by determining the mass differences between the precursor ion m/z and each of the other peaks in the spectrum and plotting the original intensity versus neutral mass. Neutral losses with small masses have limited possibilities for their composition and thus can facilitate the identification...

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...

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...

When dealing with a structure elucidation problem where little or no previous fragment information exists, the number of possibilities can seem endless. Although typically one envisions a neutral compound for the unknown, ionic compounds, such as salts and zwitterions, are also just as likely and thus can add to the complex nature of an elucidation....

When examining NMR data, it is important to understand that coupling constants and patterns can be misinterpreted. The following example is one that can be avoided. For an unknown compound, the 1H NMR spectra below shows the same coupling pattern with different interpretations for the coupling constants. Spectra A relies on chemical shifts listed at...

An unprecedented structure of Herqupenoid A containing a multicyclic, caged 2,7-dioxatetracyclo[5.4.0.04,11.05,9]hendecane fragment with an unprecedented 5/5/6/5-fused ring skeleton (molecular formula C24H34O6) was elucidated with the help of Structure Elucidator, fully automatically in 7 seconds.