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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
The approach behind solving a structure elucidation problem is very similar to attempting a math problem or working on a jigsaw puzzle. This similar mental framework shares a basis, but not limited to, on understanding the basic rules that define the problem, and in some cases the creativity and flexibility to redefine the problem. When...

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
With a monoisotopic mass identified from a mass spectrum, the next step is to fit a molecular formula (or elemental composition) to the unknown. For organic compounds, the starting elements of choice are Carbon, Hydrogen, Oxygen, Nitrogen and sometimes Sulfur. Information from starting material and known derivatives can also help when deciding what elements and...

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...