Spectrum mass

Mass spectra of most compounds can be obtained from quantities of sample as low as 1 mg. A complete mass spectrum can be recorded in far quicker time than that required for most chromatographic processes (below). 

Mass spectra (see ref 1, pp. 83-84) continue to be useful in calixarene chemistry, primarily for the determination of the molecular weights of compounds such as the parent calixarenes with n 8 and numerous other large calixarene-derived compounds e.g. a rigid cavity of nanosize dimensions ). Mass spectral deter- 

Using an ordinary El mass spectrometer with electron energies in the range 50—100 eV, the internal energy distribution, P(E), of the molecular ion is typically extremely broad (possibly tens of eV) and poorly defined. Both direct ionization and autoionization contribute to formation of molecular ions [517]. 

If either PI with monochromatic radiation or El with energy-selected electrons is employed, the maximum internal energy, Emax, which a molecular ion possesses can be controlled and known accurately. The 

Even with PI, theoretically one of the simplest ionization processes, the internal energy distribution, P(E), of the molecular ion cannot be predicted on the basis of Franck—Condon factors alone. Autoionization is well-known as being important [15, 177, 637, 640, 800], as is the more recently recognised effect of shape resonance [220, 803, 906]. It has also been shown that the onset of a decomposition can affect the energy distribution, P(E), [801, 802]. The latter effect is possibly a consequence of competition between neutral and ionic decompositions. 

Magnetic sector field instruments have mass resolutions up to m/Am = 20000 quad-rupole instruments are limited to a mass resolution of approximately m/Am = 500. For both types of instrument the a mass range extends to 500. 

High-mass resolution is needed to separate mass interferences of molecular and atom ions. Because of the mass defect of the binding energy of the nucleus, atomic ions have a slightly smaller mass than the corresponding molecular ions. To observe this typical mass resolutions between 5000 and 10000 are necessary. 

Measurement of depth profiles is based on detection of the masses of interest during sputter removal of the sample material. Such experiments have several limitations  

There are three pieces of useful information which can be obtained from mass spectroscopy the molecular mass, composition, and the fragmentation pattern of your compound. The accurate molecular mass is of primary importance since this will confirm the composition of your compound. Fragmentation information might be of value for supporting the proposed structure, possibly by comparison with known compounds. The amount required is minimal (a few mgs at most), and the material should be reasonably pure. If you are unable to obtain good microanalytical data the accurate mass measurement may provide an acceptable alternative. 

These are usually straightforward. There are various forms of melting point apparatus in widespread use, so check carefully on the procedure 

If you have distilled your product to isolate and purify it then you should already have the information required for reporting the boiling point It is important to quote the range of temperature (if observed) over which the compound distils, the pressure (measured as it is distilling), the vapour temperature (if measured), and the bath temperature. All these will be useful when you or anyone else come to repeat the work, and most of this information will be required at some time for a publication, report, or thesis. 

In contrast to the anthracyclinones [21,22], the more polar glycosides usually do not give reliable mass spectra on electron impact ionization (EI-MS). In cases such as cinerubin A (23), where aromatization can take place easily, the sugar residues are split off completely, and the bisanhydro-aglycones are formed. In the spectrum of 23, the signal of ]-pyrromycinone (24) is detected (m/z = 392). 

In contrast, fast atom bombardment (FAB), field desorption (FD), and especially electrospray ionization (ESI) usually do not give fragmentation. These are very powerful techniques in structure elucidation or derepHcation of anthracyclines, especially in combination with HPLC and MS/MS fragmentation [23] or with high resolution (HRMS). 

Both (-)- and (+)-ionization modes deliver molecular ions of sufficiently high intensity for MS/MS. In the positive mode, the [M + H], [M + Na] and sometimes also [2M-i-Na] quasimolecular ions are visible (-)-ESI delivers [M-H] and [2M-2H-I-Na] ions. In MS/MS measurements, again the high 

A mass spectrum, derived by scanning the mass filter over some predefined m/q ratio range, constitutes all the secondary ions of the polarity of interest (only one polarity can be collected at a time). Such spectra are of interest when the sample type is unknown (this allows for the identification of the elemental and/or molecirlar constituents) and/or when information on the optimal signals for the acqirisition of images and/or depth profiles is required. This option is available and commonly used in all applications of SIMS, whether in Static or Dynamic modes. 

Along with these signals are signals from all of the other isotopes of Oxygen and Silicon (relative abundances of the isotopes are defined in Appendix A.2). As the secondary ion yield for different isotopes of the same element is not 

Strongly affected in the secondary ion formation process (the effects that are noted, referred to as isotope or mass fractionation, are quantifiable as discussed in Section 33.2.23), the intensities of all isotopes follow actual isotope abundances to within a small fraction of a percent. 

In addition to the signals from all the above-listed elements are signals from various other elements. These elements, which may be intentionally introduced (examples in the semiconductor industry include Boron, Phosphorus, or Arsenic) or unintentionally introduced (these arise from exposure to some prior enviromnent) include the following Hydrogen (nominal mass of the major isotope is 1 u). Carbon (nominal mass of the major isotope is 12 u), Fluorine (nominal mass of the major isotope is 19 u). Chlorine (nominal mass of the major isotope is 35 u). 

Such interferences arise when there exist secondary ions of different elements and/or molecules that are of the same nominal mjq ratio nominal values are those rounded to the closest whole mass number). These become more prevalent  

Because the fragmentation pattern produced by a mass spectrometer can be used as a fingerprint of molecule, the mass spectrum reveals, for example, whether the correct compound has been synthesized and whether contaminants are present. One can see that it is a molecular fingerprint, just as absorption spectra are molecular fingerprints, and that it is a powerful tool for identification purposes. 

In contrast to IR and NMR spectroscopy, the principle of mass spectrometry (MS) is based on decomposition and reactions of organic molecules on theii way from the ion source to the detector. Consequently, structure-MS correlation is basically a matter of relating reactions to the signals in a mass spectrum. The chemical structure information contained in mass spectra is difficult to extract because of the complicated relationships between MS data and chemical structures. The aim of spectra evaluation can be either the identification of a compound or the interpretation of spectral data in order to elucidate the chemical structure [78-80], 

Other methods consist of algorithms based on multivariate classification techniques or neural networks they are constructed for automatic recognition of structural properties from spectral data, or for simulation of spectra from structural properties [83]. Multivariate data analysis for spectrum interpretation is based on the characterization of spectra by a set of spectral features. A spectrum can be considered as a point in a multidimensional space with the coordinates defined by spectral features. Exploratory data analysis and cluster analysis are used to investigate the multidimensional space and to evaluate rules to distinguish structure classes. 

Multivariate data analysis usually starts with generating a set of spectra and the corresponding chemical structures as a result of a spectrum similarity search in a spectrum database. The peak data are transformed into a set of spectral features and the chemical structures are encoded into molecular descriptors [80]. A spectral feature is a property that can be automatically computed from a mass spectrum. Typical spectral features are the peak intensity at a particular mass/charge value, or logarithmic intensity ratios. The goal of transformation of peak data into spectral features is to obtain descriptors of spectral properties that are more suitable than the original peak list data. 

Spectral features and their corresponding molecular descriptors are then applied to mathematical techniques of multivariate data analysis, such as principal component analysis (PCA) for exploratory data analysis or multivariate classification for the development of spectral classifiers [84-87]. Principal component analysis results in a scatter plot that exhibits spectra-structure relationships by clustering similarities in spectral and/or structural features [88, 89]. 

DENDRAL proved to be fundamentally important in demonstrating how rule-based reasoning could be developed into powerful knowledge-engineering tools [93]. 

These are discussed in (B-71MS4). Oxirane itself shows a strong molecular ion peak and a slightly stronger base peak at mje 29 (CHO ) due to isomerization to ethanal and loss of a methyl radical. Substituted oxiranes tend to show only weak molecular ion peaks, because of rearrangement and fragmentation. 

Matrix-assisted laser desorption ionization (MALDI) 

Collision of electron beam with molecule, causing ejection of electrons Collision of beam of neutral atoms with solid sample 

High voltage yields aerosol of electrically charged droplets Plasma created by corona discharge causes gas phase ion- molecule reactions 

UV laser pulse applied to solid matrix containing sample 

Very soft technique, little fragmentation useful for molecules of very high mass Soft technique, little fragmentation 

---

Mass spectra from a carbon cluster ion source show strong magic numbers at C, and C d[136]. This led to the... 

Rosenstock H M, Wallenstein M B, Wahrhaftig A L and Frying H 1952 Absolute rate theory for isolated systems and the mass spectra of polyatomic molecules Proc. Natl Acad. Sci. USA 38 667-78... 

Mies F H and Krauss M 1966 Time-dependent behavior of activated molecules. High-pressure unimolecular rate constant and mass spectra J. Cham. Phys. 45 4455-68... 

The mass spectrometer tends to be a passive instrument in these applications, used to record mass spectra. In chemical physics and physical chemistry, however, the mass spectrometer takes on a dynamic function as a... 

Figure Bl.7.10. Tliree mass spectra showing the results of reactive collisions between a projectile ion C H. NH, isomeric butenes. (Taken from Usypchiik L L, Harrison A G and Wang J 1992 Reactive...

Figure Bl.7.16. Mass spectra obtained with a Finnigan GCQ quadnipole ion trap mass spectrometer, (a)...

This is the domain of structure elucidation, which, for most part, utilizes information from a battery of spectra (infrared, NMR, and mass spectra). 

The DENDRAL project initiated in 1964 at Stanford was the prototypical application of artificial intelligence techniques - or what was understood at that time under this name - to chemical problems. Chemical structure generators were developed and information from mass spectra was used to prune the chemical graphs in order to derive the chemical structure associated with a certain mass spectrum. 

The large databases CA, Betlstein, and Gmelin do not provide methods for directly searching spectroscopic data. Detailed retrieval of spectroscopic information is provided in databases that contain one or more types of spectra of chemical compounds. Section 5.18 gives an ovei view of the contents of larger databases including IR, NMR, and mass spectra. 

Specinfo, from Chemical Concepts, is a factual database information system for spectroscopic data with more than 660000 digital spectra of 150000 associated structures [24], The database covers nuclear magnetic resonance spectra ( H-, C-, N-, O-, F-, P-NMR), infrared spectra (IR), and mass spectra (MS). In addition, experimental conditions (instrument, solvent, temperature), coupling constants, relaxation time, and bibliographic data are included. The data is cross-linked to CAS Registry, Beilstein, and NUMERIGUIDE. 

The second step, the so called generation, created only those structures which complied with the given constraints, and imposed additional restrictions on the compounds such as the number of rings or double bonds. The third and final phase, the tester phase, examined each proposed solution for each proposed compound a mass spectrum was predicted which was then compared with the actual data of the compound. The possible solutions were then ranked depending on the deviation between the observed and the predicted mass spectra. 

Correlations between structure and mass spectra were established on the basis of multivariate analysis of the spectra, database searching, or the development of knowledge-based systems, some including explicit management of chemical reactions. 

F.W McLafferty, R.H. Hertel, Org. Mass Spectrom. 1994, 8, 690-702. Probability-based matching of mass spectra. 

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,... 

The mass spectra of 2-aminothiazole and 2-amino-4-methylthiazole are characterized by the following peaks (136). 

Co(II), Ni(n), Cu(n), and Zn(II) complexes of Schiff bases derived from 4-aryl-2-aminothiazoles and salicylaldehyde have been prepared, and structure 276 (Scheme 170) was established by magnetic susceptibility measurements and by infrared, electronic, and mass spectra (512). 

The mass-spectrometric fragmentation of 2-aminothiazole-3-oxides is characterized by the abstraction of O and OH out of the molecule ion. Variations observed in the mass spectra suggest an equilibrium between tautomers 354a and 354b in the gas phase (Scheme 203). 

Perfused rat liver rapidly converts 4-m thyI-5-/3-chloroethy]thiazole to 2-hydroxy -4-methylthiazol-5-y) acetic acid (40. 41). Finally, tw o new human metabolites of chlormethiazole have been isolated and identified by mass spectra as 2-hydroxy-4-methyl-5-/S-chloroethylthiazole and 2-hydroxy-4-methyl-5-ethylthiazole (42). 

The 4-Hydroxy-thiazoles are characterized by infrared absorption near 1610 cm (KBr) (3) or 1620 to 16.S0cm (CCI4) (8), indicating a strongly polarized carbonyl group. H-5 resonates near 5.6 ppm in the NMR spectrum like similar protons in other mesoionic compounds (3). Two fragmentations of the molecular ion are observed in the mass spectra. The first involves rupture of the 1,2 and 3,4 bonds with loss of C2R 0S . In the second, the 1,5 and 3,4 bonds are cleaved with elimination of C2R 0. ... 

The reasonable stable products are characterized by an ir-absorption near 1615 cm". The 4-protons resonate near 6.2 ppm in the H NMR spectrum (23). NMR spectra exhibit a carbonyl atom signal near 173 ppm, whereas C-4 resonates near 8 108 these positions are characteristic of other mesoionic ring carbon atoms (24). In the mass spectra, decomposition with loss of CO, rupture of the 1,5 and 2.3 bonds with elimination of R NC2R 0 and cleavage of the 1,2 and 3,4 bonds with elimination of C2R 0S is observed (11)... 

The mass spectra of more substituted thiazoles, or those with larger alkyl groups are more complex and involve other fragmentation patterns (117, 118, 374). The molecular ion is still abundant but decreases with increasing substitution past the ethyl group. 

---