Mass spectrometry structure elucidation

The role of functional groups in directing molecular fragmentation, and the value of mass spectrometry in elucidation of the structure of organic compounds was clearly demonstrated by Biemann [28], Beynon [29], and McLafferty [30]. 

FTMS also has the potential of becoming an important tool for determining molecular structure. Traditionally, mass spectrometry has been rather limited in its ability to determine the structure of an unknown compound unambiguously. Additional structural methods, such as nuclear magnetic resonance or crystallography, are commonly used in conjunction with mass spectrometry to elucidate the identity of a molecule. However, when the amount of sample is severely limited or when the sample is a component in a complex mixture, mass spectrometry is often one of the few analytical techniques that can be used. 

The previous discussion has referred to photolysis and thermolysis only. Many of the transformations described have also been observed on mass spectrometry of isoxazoles, although it is not always clear whether they occur as a result of electron impact or by prior thermal reaction.211-212 It should be noted that such reactions can create problems in the use of mass spectrometry for elucidating the structures of isoxazoles. 

Mass spectrometry is a convenient method for identifying structures of compounds, either in their pure form or in mixtures. It should be noted that in mass spectrometry structure refers to atom and group connectivity, rather than to bond distances and bond angles. Also, the elucidation of structures of ions is performed by inducing their chemical transformations and detecting the reaction products. In other words, a mass spectrometer should be considered as a mini-chemical laboratory, in which ions can be produced and their structure and reactivity can be studied. 

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],... 

H. Budzikiewicz, C. Djerassi and D. H. Williams, Structure Elucidation of Natural Products by Mass Spectrometry, Holden-Day, San Francisco, 1964, Volume 1, Chapter 2. 

Other methods of identification include the customary preparation of derivatives, comparisons with authentic substances whenever possible, and periodate oxidation. Lately, the application of nuclear magnetic resonance spectroscopy has provided an elegant approach to the elucidation of structures and stereochemistry of various deoxy sugars (18). Microcell techniques can provide a spectrum on 5-6 mg. of sample. The practicing chemist is frequently confronted with the problem of having on hand a few milligrams of a product whose structure is unknown. It is especially in such instances that a full appreciation of the functions of mass spectrometry can be developed. 

This tool has been of great value in the elucidation of the structures of some important biologically-derived amino (14) and deoxy (13) sugars in the form of their dialkyl dithioacetals. Tedious degradation reactions which would require both time and valuable material could be avoided in many cases by resorting to mass spectrometry. The antibiotic sugars (22) paramose (1), mycinose (2) and chalcose (3) were, for example, studied by mass spectrometry (13, 14). 

Ibid., Structure Elucidation of Natural Products by Mass Spectrometry,... 

The great strength of mass spectrometry as a technique is that it can provide both the molecular weight of an analyte (the single most discriminating piece of information in structure elucidation) and information concerning the structure of the molecule involved. 

Table 5.7 Theoretically predicted polypeptides from the trypsin digestion of S-lacto-globulin (/3LG) . Reprinted from J. Chromatogr., A, 763, Turula, V. E., Bishop, R. T., Ricker, R. D. and de Haseth, J. A., Complete structure elucidation of a globular protein by particle beam liquid chromatography-Fourier transform infrared spectrometry and electrospray liquid chromatography-mass spectrometry - Sequence and conformation of /3-lactoglobulin , 91-103, Copyright (1997), with permission from Elsevier Science...

Figure 5.45 Structures of (1) Bosentan (C27H29N5O6S [M + H]+ 552.1917) and three of its metabolites, formed by (2) oxidation (C27H29N5O7S [M + H]+ 568.1866), (3) demethylation (C26H27N5O6S [M- -H]+ 538.1760), and (4) demethylation-oxidation (C26H27N5O7S [M + M]+ 554.1709). Reprinted by permission of Elsevier Science from Exact mass measurement of product ions for the structural elucidation of drug metabolites with a tandem quadrupole orthogonal-acceleration time-of-flight mass spectrometer , by Hopfgartner, G., Chemushevich, I. V., Covey, T., Plomley, 1. B. and Bonner, R., Journal of the American Society for Mass Spectrometry, Vol. 10, pp. 1305-1314, Copyright 1999 by the American Society for Mass Spectrometry.

The structures of many oligosaccharide chains can be elucidated by gas-liquid chromatography, mass spectrometry, and high-resolution NMR spectrometry. Glycosidases hydrolyze specific linkages in oligosaccharides and are used to explore both the structures and functions of glycoproteins. 

The following is a procedure recommended for elucidating the structure of complex organic molecules. It uses a combination of different NMR and other spectroscopic techniques. It assumes that the molecular formula has been deduced from elemental analysis or high-resolution mass spectrometry. Computer-based automated or interactive versions of similar approaches have also been devised for structural elucidation of complex natural products, such as SESAMI (systematic elucidation of structures by using artificial machine intelligence), but there is no substitute for the hard work, experience, and intuition of the chemist. 

Other spectroscopic properties such as nuclear magnetic resonance (NMR), mass spectrometry (MS), infra-red (IR), and circular dichroism (CD) spectra of chlorophyll compounds and derivatives have been valuable tools for structural elucidation. - ... 

The development and reports of methods for colorless chlorophyll derivative (RCCs, FCCs, and NCCs) analysis are relatively recent and the structures of the compounds are being elucidated by deduction from their chromatographic behaviors, spectral characteristics (UV-Vis absorbance spectra), mass spectrometry, and nuclear magnetic resonance analysis. The main obstacle is that these compounds do not accumulate in appreciable quantities in situ and, moreover, there are no standards for them. The determination of the enzymatic activities of red chlorophyll catabolite reductase (RCCR) and pheophorbide a monoxygenase (PAO) also helps to monitor the appearance of colorless derivatives since they are the key enzymes responsible for the loss of green color. ... 

Gelsevirine (2) was first isolated in 1953 from G. sempervirens as a minor component (3). Its structure was later elucidated on the basis of mass spectrometry as well as H-NMR and 13C-NMR studies (4). Gelsevirine has been found to be the predominant alkaloid in G. rankinii (24), and it was claimed that some of the previously reported 1 H-NMR and 13C-NMR data should be revised. Thus the previous assignments of H-16, H-15, H-14a, H-14e, and H-6 for gelsevirine should be changed to H-15, H-14a, H-16, H-6, and H-14e, respectively, from the evidence of the more accurate homonu-clear 2D COSY experiments. Similarly, from the heteronuclear 2D correlation spectrum, the assignments for C-16, C-15, C-6, and 1V-CH3 should be revised to C-15, C-16,1V-CH3, and C-6, respectively. 

Several modem analytical instruments are powerful tools for the characterisation of end groups. Molecular spectroscopic techniques are commonly employed for this purpose. Nuclear magnetic resonance (NMR) spectroscopy, Fourier transform infrared (FTIR) spectroscopy and mass spectrometry (MS), often in combination, can be used to elucidate the end group structures for many polymer systems more traditional chemical methods, such as titration, are still in wide use, but employed more for specific applications, for example, determining acid end group levels. Nowadays, NMR spectroscopy is usually the first technique employed, providing the polymer system is soluble in organic solvents, as quantification of the levels of... 

Two-dimensional (2D) NMR is irrefutably the cornerstone of modem structure elucidation methods.1 Despite the inherently low sensitivity of NMR compared to other forms of analytical spectroscopy such as mass spectrometry and vibrational spectroscopy, NMR methods provide the means of establishing atom-to-atom connectivities that cannot be established by other methods. Supplemented by accurate mass measurements and fragmentation pathway information, NMR data can facilitate the elucidation of most small molecule structures. 

In the present chapter, we first provide some general information concerning the chemistry of waxes and lipids currently encountered in various items from our cultural heritage and we detail the main protocols based on direct mass spectrometry that have been developed so far. We then discuss the mass spectra obtained by EI-MS on a range of reference substances and materials sampled from museum and archaeological artefacts. We then focus on the recent possibilities supplied by electrospray ionisation for the elucidation of the structure of biomarkers of beeswax and animal fats. 

Hence, direct mass spectrometry techniques, either using El or ESI, appear to be powerful and innovative analytical tools for elucidating the structure of the main biomarkers present in a wide range of waxes and lipids that may be preserved in archaeological objects and in museum works of art. In most cases, they have nevertheless to be cautiously exploited in combination with other complementary analytical techniques. 

Y.Y. Soong and P.J. Barlow, Isolation and structure elucidation of phenolic compounds from longan (Dimocarpus longan Lour.) seed by high performance liquid chromatography electrospray ionization mass spectrometry, J. Chromatogr. A, 1085, 270 277 (2005). 

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