Molecular spectral interpretation

In conclusion, SSIMS spectra provide not only evidence of all the elements present, but also detailed insight into molecular composition. Quasimolecular ions can be desorbed intact up to 15000 amu, depending on the particular molecule [3.17] and on whether an effective mechanism of ionization is present. Larger molecules can be identified from fragment peak patterns which are characteristic of the particular molecules. If the identity of the material being analyzed is completely unknown, spectral interpretation can be accomplished by comparing the major peaks in the spectrum with those in a library of standard spectra. 

Recent attention has focused on MS for the direct analysis of polymer extracts, using soft ionisation sources to provide enhanced molecular ion signals and less fragment ions, thereby facilitating spectral interpretation. The direct MS analysis of polymer extracts has been accomplished using fast atom bombardment (FAB) [97,98], laser desorption (LD) [97,99], field desorption (FD) [100] and chemical ionisation (Cl) [100]. 

C 1-NMR spectroscopy is the method of choice for determining the molecular structure of polymers in solution [230]. Polyolefin 13C NMR is mainly quantitative ID 1-NMR multiple pulse techniques are used for spectral interpretation. The resolution obtained in 13C NMR spectra of LDPE is an order of magnitude larger than in the corresponding 1H-NMR spectra... 

Mass spectrometry is used to identify unknown compounds by means of their fragmentation pattern after electron impact. This pattern provides structural information. Mixtures of compounds must be separated by chromatography beforehand, e.g. gas chromatography/mass spectrometry (GC-MS) because fragments of different compounds may be superposed, thus making spectral interpretation complicated or impossible. To obtain complementary information about complex mixtures as a whole, it may be advantageous to have only one peak for each compound that corresponds to its molecular mass ([M]+). Even for thermally labile, nonvolatile compounds, this can be achieved by so-called soft desorption/ionisation techniques that evaporate and ionise the analytes without fragmentation, e.g. matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS). 

Fig. 11.3. Electron ionization and methane Cl mass spectra of toluene. The key features of the respective mass spectra are labeled. Spectral interpretation is based on recognition and understanding of these key features and how they correlate with structural elements of the analyte molecule of interest. The signal representing the most abundant ion in a mass spectrum is referred to as the base peak, and may or may not be the molecular ion peak (which carries the molecular mass information). Cl spectra provide confirmation of molecular mass in situations where the El signal for the molecular ion (M+ ) is weak or absent. The Cl mass spectrum provides reliable molecular mass information, but relatively little structural information (low abundance of the fragment ions). Compare with Fig. 11.4.

Crosscheck proposed molecular structure and mass spectral data. This is also recommended between the single steps of mass spectral interpretation. 

The occurrence of [Mh-H] ions due to bimolecular processes between ions and their neutral molecular counterparts is called autoprotonation or self-CI. Usually, autoprotonation is an unwanted phenomenon in EI-MS. [M-i-1] ions from autoprotonation become more probable with increasing pressure and with decreasing temperature in the ion source. Furthermore, the formation of [M-i-1] ions is promoted if the analyte is of high volatility or contains acidic hydrogens. Thus, self-CI can mislead mass spectral interpretation either by leading to an overestimation of the number of carbon atoms from the C isotopic peak (Chap. 3.2.1) or by... 

Identification of the different types of ions observed in a mass spectrum through peak-matching and metastable ion analysis allows the determination of molecular structure. Several newer mass spectrometric techniques Mass analysed ion kinetic energy (MIKE) or reversed Nier-Johnson geometry) can also be used in spectral interpretation. These techniques are described in specialised monographs. 

Although some of the assignments of the bands in the spectrum of PETP cannot be made with great certainty at this time, it appears that the main outlines of a satisfactory spectral interpretation have been established. At least the problems involved in achieving this now stand out more clearly. As has been noted in the previous discussion, these assignments hold the key to a deeper understanding of the molecular chain structure, both in the crystalline and in the amorphous phases. 

Structural Information from Spectral Data. The kinds of information that can be derived from an unknown mass spectrum by either human or computer examination include the identities of substructural parts of the molecule (parts that both should, and should not, be present), data concerning the size of the molecule (molecular weight, elemental composition), and the reliability of each of these postulations. In our opinion, the latter is much more critical for mass-spectral interpretive algorithms than those for techniques such as NMR and IR the effect of a particular substructure on the mass spectrum is often dependent on other parts of the molecule, and a thorough understanding of these effects can only be achieved by studying the spectra of closely related molecules. 

Intermolecular relaxation effects are a central issue in the interpretation of the ultraviolet photoelectron spectroscopy (UPS) of molecular solids. These relaxation effects result in several significant characteristics of UPS valence spectra, intermolecular relaxation phenomena lead to localized electron molecular-ion states, which are responsible for rigid gas-to-solid molecular spectral energy shifts, spectral line broadening, and dynamic electronic localization effects in aromatic pendant group polymers. 

Tossell, J. A. (1973). Molecular orbital interpretation of x-ray emission and ESCA spectral shifts in silicates. J. Phys. Chem. Solids 34, 307-19. 

The second problem is that ion-ion or ion-neutral reactions can occur. Reactions (e.g., proton transfer) result in high abundance of protonated molecular ions in the mass spectrum. Thus QIT can be disadvantageous for determining chemical composition in manual spectral interpretation, because the presence of the (M + l)" ion tends to confuse the interpretation. Library spectral matching, however, is not affected if the spectral matching algorithm reflects the unique features of the QIT spectrum. An external ionization source with ion injection into the QIT is an alternative solution, because only ions are present in the trap (i.e., neutral analyte molecules that could participate in ion-molecule reactions are not present). The Thermo Finnigan PolarisQ GC/MS is an example of such an instrument. 

Synthesis control has two tasks directly associated with it. These are to identify or verify the identity of a combinatorial component and to determine the purity of the synthetic product. When characterizing a parallel library it is a relatively easy task to obtain a molecular weight from a small amount (femto-mole) of compound and thereby obtain a crude identification of the product. This circumvents the need to perform more difficult NMR or IR spectral interpretation and sample introduction maybe performed by a simple flow-injection atmospheric pressure ionization (API)/MS system. Purity assessment is typically based on area percentage normalization of the total ion chromatogram, assuming equivalent ionization of impurities and parent compounds, or a secondary detector, such as UY... 

A compilation of the spectral properties of two pyrrolol 1,2-c]-pyrimidines is presented in Table II. Theoretical molecular orbital interpretations of the electronic spectra of pyrrolol l,2-c]pyrimidines have also been reported.51... 

An El spectrum comprises a mixture of ions of types A and C which may contain some molecular ion (Fig. 5.3). To complicate matters, the ions A and C may also fragment further to produce smaller ions. In these processes, the ion which fragments is known as the precursor or parent ion, whilst the smaller ions formed are known as the product ions. Understanding the relationship between precursor and product ions is at the heart of mass spectral interpretation and deducing the structure of the original molecule. A simple example is shown (Fig. 5.4). 

---