Simulation of mass spectra

Schechter, and Zander C125, 260, 261, 3593 applied a set of binary classifiers to predict the mass spectra of compounds from the known molecular structures. This approach is completely empirical and does not assume any mass spectrometric knowledge of fragmentation of ions. 

Each compound was described by a set of about 100 descriptors. The descriptors were generated from a fragmentation code or a coded structure (connection table). The set of descriptors is used as a pattern vector that characterizes a compound. Learning machine C261, 3593 and an iterative least-squares method C2603 have been used to train binary classifiers that predict mass spectral peak presence or absence at certain mass numbers. 60 classifiers for 60 mass numbers predict whether the peak is greater than 0.5 % of the total ion current. (The total ion current is the sum of all peak heights in a spectrum.) For 11 of these mass numbers 

The method was proposed for an automatic interpretation of unknown mass spectra. If a set of possible compounds is assumed for the unknown, artificial mass spectra can be calculated and compared with the mass spectrum of the unknown. The compound associated with the artificial spectrum which compared most closely would then be assumed to be the compound producing the unknown spectrum. However, successful generation of suitable classifiers for more mass numbers and more intensity cutoffs would require very large data sets. 

Numerical values of classifiers have been reported only in a few papers C129, 163, 165, 1923. 

By analogy with mass chromatograms, this graph was called classification chromatogram . 

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J. Gasteiger, W. Hanebeck, K.-P. Schultz, S. Bauerschmidt, R. Hollering, Automatic analysis and simulation of mass spectra, in Computer-Enhanced Analytical Spectroscopy, Vol. 4,... 

A reactor is defined as a container where reactions occur at the same time. These containers are a generic concept of an entity that stores the reaction. In the real world, these are equivalent to a physical container like a flask, a reaction tank, or the fragmentation space in a mass spectrometer. Each change in a reaction requires a new reactor to be instantiated. Eor instance, if starting materials are added to a container and the mixture is then heated, EROS requires two reactors one for the reactant entry and another for the heating period, where no further substances are added. Also the simulation of mass spectra using MASSIMO algorithms is performed in an individual reactor. 

Montaudo, M.S., Ballistreri, A., and Montaudo, G., Determination of Microstructure in Copolymers. Statistical Modeling and Computer Simulation of Mass Spectra, Macromolecules, 24, 5051 (1991). 

H.B. Woodruff, P.C. Tway, and J. Cline Love, Factor analysis of mass spectra from partially resolved chromtographic peaks using simulated data, Anal. Chem., 53 81 (1981). 

Fig. 11. Abundance mass spectra of differently charged hot CgoLL clusters evaporating atoms calculated with a Monte-Carlo simulation (the Li and Cgg isotope distributions are included). Energies required to remove Li atoms were calculated using the MNDO method. The peaks at x = 12 and at x = 6 + n (where n is the cluster charge) observed in experiment (Fig. 9) are well reproduced.

Boylan and Tripp [76] determined hydrocarbons in seawater extracts of crude oil and crude oil fractions. Samples of polluted seawater and the aqueous phases of simulated samples (prepared by agitation of oil-kerosene mixtures and unpolluted seawater to various degrees) were extracted with pentane. Each extract was subjected to gas chromatography on a column (8 ft x 0.06 in) packed with 0.2% of Apiezon L on glass beads (80-100 mesh) and temperatures programmed from 60 °C to 220 °C at 4°C per minute. The components were identified by means of ultraviolet and mass spectra. Polar aromatic compounds in the samples were extracted with methanol-dichlorome-thane (1 3). 

Fig. 11.17. Simulated mass chromatograms resulting from precursor ion and constant neutral loss tandem mass spectra (middle and bottom traces), illustrating the selectivity that those MS/MS scan modes can bring to chromatographic analyses. The top trace in the figure represents a total ion chromatogram obtained using a conventional single stage of mass analysis.

W. Windig, P. G. Kistenmaker, and J. Haverkamp, Chemical interpretation of differences in pyrolysis—Mass spectra of simulated mixtures of biopolymers by factor analysis with graphical rotation, J. Anal. Appl. Pyrolysis 3(3), 199-212 (1981/1982)... 

Gas-Solid Chromatography and Mass Spectrometry. The cuts trapped out from the simulated distillations were rechromatographed on lithium chloride-coated silica columns (4). The column effluent was split with a portion directed to a flame ionization detector and the other to the mass spectrometer in a ratio of 1 4. This chromatographic step greatly facilitated the interpretation of the mass spectra. In many cases it appeared as though pure compounds were obtained. Only some of these gas-solid chromatograms will be discussed. 

Water clusters containing simple ions are another area of current experimental and theoretical interest. Accordingly, they are also the subject of EA studies. Chaudhury et al. [113] have used EA methods on empirical potentials to obtain optimized structures of halide ions in water clusters, which they then subjected to AMI calculations for simulation of spectra. EA applications to alkali cations in TIP4P water clusters [114,115] have led to explanations of experimental mass-spectroscopic signatures of these systems, in particular the lack of magic numbers for the sodium case and some of the typical magic numbers of the potassium and cesium cases, and the role of dodecahedral clathrate structures in these species. 

Pyrolysis of polyisoprene takes place by a free radical mechanism and generates mainly isoprene (MW=68), a dimer of isoprene (DL-limonene, MW=138), and several other unsaturated hydrocarbons (see Sections 2.6 and 6.1). The mass spectra fragmentation (generating fragments with specific mass/charge (m/z) ratios) of a model molecule simulating polyisoprene (isoprene oligomer) occurs by the mechanisms as indicated below ... 

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