Skip To Content

ACD/Labs Blog

Arvin Moser
Like bromine, compounds that contain chlorine atoms have a distinct ion pattern on a mass spectrum. The A+2 peak for a monochlorinated compound will be at almost one-third the intensity to the 35Cl peak due to the presence of 37Cl isotope. A compound with two chlorine atoms will show distinct A+2 and A+4 peaks with...

Arvin Moser
When the incorrect number of directly-bonded protons are assigned to carbons, the elucidator is left with extra protons. (This can happen in situations with a highly-crowded region on a 1H NMR spectrum.) Where possible, tallying the expected number of exchangeable protons can serve as a warning flag that something is amiss. The following carbons, shown...

Arvin Moser
The 1H-13C HMQC, HSQC, DEPT-HSQC, HSQC-TOCSY and HETCOR experiments offer the elucidator information on the proton-carbon connectivity. The interpretation process comes down to 3 basic assignments: the correlation belongs to a methyl, methylene or methine carbon. A methyl or methine carbon exhibits at most a single correlation between the 1H and 13C axes. A methylene...

Arvin Moser
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...

Arvin Moser
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...

Arvin Moser
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...

Arvin Moser
Although NMR offers some strategies for determining the presence of a fluorine atom(s), fragment loss of a CF3 group can be determined from a mass spectrum. The EI MS for 2,2,2-trifluoro-N,N-dimethylacetamide (Mmi = 141 Da) is shown below. The ion peak at m/z 72 indicates the loss of a CF3 group. Although the ion peak...

Arvin Moser
A very useful bit of information on the proton count comes from integrating a 1H NMR spectrum. However, overlapping resonances can make integration less than straightforward and in some cases ambiguous. Integration involves the following decisions to be made by the elucidator: which resonances to integrate, where the integral begins and ends, and what the...

Arvin Moser
Looking for the next big pharmaceutical drug among natural products is a growing endeavour. However, a common drawback to working with natural products is the limited amount of sample. With a sample limitation, acquiring a 13C NMR spectrum within a reasonable time can be an issue. Rather than wasting instrument time on a 13C NMR,...