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ACD/Labs Blog

Arvin Moser
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...

Arvin Moser
A previous blog described how a sodiated ion peak can be used to locate or calculate the molecular ion for an unknown compound. In a similar fashion, the dimer ion peak can be used to identify the mass of the unknown even if the molecular ion is no visible. The ESI+ MS data below shows...

Arvin Moser
Depending on sample preparation, adduct ions can be present on a mass spectrum. The goal of the elucidator is to identify whether an adduct ion(s) is present and its contribution to the mass (or elemental composition) of the unknown compound. The example ESI+ mass spectrum below exhibits 2 ion clusters at m/z 951.305 and 973.287,...

Arvin Moser
With a well-tuned and calibrated, high resolution MS instrument, a molecular formula(e) can be devised from the m/z for an ion peak. In cases where more than one molecular formula fits, knowing the accuracy of the MS instrument can help in narrowing down the choices. The first step is to identify the molecular ion peak...

Arvin Moser
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...

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
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 best use of a set of tools for a structure elucidation are those that have a general target or goal in mind. Random experiments for the sake of collecting data are a sure sign of inexperience. With that said, Infrared (IR) spectroscopy is a great tool for identifying or confirming a functional group(s). It...

Arvin Moser
MS and NMR are complementary tools for structure elucidation. Knowing when to apply which tool can assist an elucidator in solving for an unknown structure quickly and with less frustration. Although the sample data below is for a simple organic structure, it is working through many simple examples that one refines the skills needed for...

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...