Mass spectra, unknown, molecular structure elucidation

Figure 14 Application of spectra classification results in systematic structure elucidation. Given data for an unknown molecular structure are the molecular formula and the low resolution mass spectrum. MOLGEN is an isomer generator program, MSclass is a program for the automatic recognition of some substructures. The total number of isomers is 596. From the mass spectrum a substructure that has to be present (goodlist) and a substructure that has to be absent (badlist) was recognized. The final result consists of seven molecular candidate structures. [Reproduced from Ref. 103 with kind permission of Gesellschaft Deutscher Chemiker]...

There are two limitations of electron impact ionization, which in other ways is nearly an ideal ion source for identification of organic compounds. The sample must be stable as neutral molecules in the gas phase prior to ionization. There are many compounds, however, that are simply not stable at the temperatures required for vaporization. Radical molecular ions are formed with excess energy that may be sufficient for complete elimination of molecular mass information from the mass spectrum, even at low electron energies (e.g. 15-20 eV). Molecular mass information is almost always required for structure elucidation of unknown compounds. A softer ionization technique, such as chemical ionization, may be used in these circumstances to establish the compound molecular mass. 

One of the most important pieces of information required to elucidate the molecular structure of an unknown organic compound is its molecular mass, which provides a window within which the elemental composition and the final structure of the compound must fit. Therefore, the first essential step to identifying a compound is to measure its molecular mass by determining the m/z value of the molecular ion. Molecular mass measurements can be performed at either low or high resolution. A low-resolution measmement provides information about the nominal mass of the analyte, and its elemental composition can be also determined for low-molecular-weight compounds from the isotopic pattern. From a high-resolution mass spectrum, the accurate molecular mass can be determined, from which it is also feasible to deduce the elemental composition. Chemists who work with synthetic compounds and natural products rely heavily on the exact mass measurement data for structmal assignment. This value is acceptable in lieu of the combustion or other elemental analysis data. An acceptable value of the measured mass should be within 5 ppm of the accmate mass [1]. As shown below, the mass measurement error is reported either in parts per million (ppm) or in millimass units (mmu). 

Consequently, structure elucidation is required to obtain more insight into the new compound. In this task, MS also plays a crucial role, as often the quantities are too low to enable straight-forward identification via NMR. The EI-MS spectrum can be very informative, but is often not sufficient by itself to provide a positive identification. Chemical ionization can be used to determine the molecular weight of the unknown, especially for molecules that exhibit extensive fragmentation during El. In addition, accurate mass measurements with sector or Time... 

MS-MS in the product-ion scan mode is generally quite successful in structure elucidation of unknowns. There are ample examples available in the literature. However, the interpretation of the production mass spectrum is not always straightforward. When a protonated molecule is selected as precursor ion, the fragmentation rules significantly differ from the well-known fragmentation rules valid for molecular ions generated by electron ionization. Upon fragmentation, protonated molecules have a... 

The universality of El (aU organic molecules are ionizable by the process) justifies the success of this technique, which is by far the most used in GC-MS coupling. It nevertheless happens that this techniqne is unsuitable for certain analyses. In structural elucidation, the fact that the molecular ion is not always present poses a crucial problem. Indeed, the interpretation of a mass spectrum implies establishing the observed fragmentations from a molecular ion. Confronted with the electron ionization spectrum of an unknown product, it is difficult if not impossible to start the interpretation since one cannot know whether the highest m/z ratio present in the spectrum corresponds to the molecular ion or not. Chemical ionization (see next section) is very valuable in... 

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