Source structure assignment

Compound quality is addressed with a rapid LC/UV/MS assay [12]. Many groups use compounds that were synthesized several years before or obtained from an outside source. Structure assignment inaccuracies, impurities, and degradants can cause SAR and SPR confusion for the drug-discovery team. 

The ionization techniques most widely used for LC-MS, however, are termed soft ionization in that they produce primarily molecular species with little fragmentation. It is unlikely that the molecular weight alone will allow a structural assignment to be made and it is therefore desirable to be able to generate structural information from such techniques. There are two ways in which this may be done, one of which, the so-called cone-voltage or in-source fragmentation, is associated specifically with the ionization techniques of electiospray and APCl and is discussed later in Section 4.7.4. The other, termed mass spectrometry-mass spectrometry (MS-MS) or tandem mass spectrometry, is applicable to all forms of ionization, provided that appropriate hardware is available, and is described here. 

On the other hand, some compounds which are Included may not be true Gossypium secondary metabolites. Not only are the sources mentioned above possible contributors of exogenous compounds which have been Included in the accompanying Tables (I - X), but also it is quite possible that methods of isolation and analysis caused molecular transformation which created Isomers of true metabolites or even caused more drastic alterations. The diversity of structures which are plausible natural products is so great that it is not reasonable to exclude many of those reported simply on the basis of structure assignment. For this reason, it can be expected that some errors of inclusion have been made. 

Carbazole (1) was isolated first from the anthracene fraction of coal tar in 1872 by Graebe and Glaser (12). In 1987, almost a century later, Bhattacharyya et al. reported for the first time the isolation of carbazole (1) from a plant source, Glycomis pentaphylla (13) (Scheme 2.1). Structural assignment of carbazole (1) was based on UV, IR, and mass spectral data, as well as direct comparison with an authentic sample. 

In 1997, Chakrabarty et al. reported the isolation of 9-carbethoxy-3-methylcarba-zole (5) and 9-formyl-3-methylcarbazole (6) from the roots of M. koenigii (17). These metabolites are the first 9-formyl and 9-carbethoxy carbazole derivatives obtained from plant sources. 9-Formyl-3-methylcarbazole (6) showed weak cytotoxicity against both mouse melanoma B16 and adriamycin-resistant P388 mouse leukemia cell lines. The structural assignment of these two alkaloids was based on the IR- and H-NMR spectra which were lacking any signal of an NH group. Additional structural support for 9-carbethoxy-3-methylcarbazole (5) was provided by the similarity of the UV absorption spectrum with that of a synthetic sample, obtained by reaction of 3-methylcarbazole with ethyl chloroformate in the presence of base. Further structural support for 9-formyl-3-methylcarbazole (6) was derived from a comparison of the UV spectrum and the IR carbonyl absorption (1696 cm ) with those of an authentic sample of 9-formyl-3-methylcarbazole (1700 cm ), prepared by the treatment of 3-methylcarbazole (2) with 98% formic acid (17) (Scheme 2.3). 

Laureacetal-B (70) is a tricyclic oxetane recently isolated from a marine alga. It has the interesting features of bromine substitution and a cyclic acetal structure. In view of the extreme ease of hydrolysis of 2-methoxyoxetane, it seems surprising that a strained ring cyclic acetal would be isolated from a marine source. Its structure assignment is based on spectral studies and chemical transformations (79CL301). 

In this reaction the source of the azoxy oxygen appears to be the nitroso group [6]. The preparation of t-butyl-OAW-azoxymethane (iV-methyl-A -t-butyldiazine jV -oxide) is an example of preparation of an unsymmetrical azoxy compound which is quite generally applicable. The structure assignment is based on NMR data. 

Source Reprinted with permission from Ackermann et al., 1996a. Copyright 1996 Elsevier. Note n.a. = not applicable n.d. = not detected unk = unknown. a See histogram in Figure 6. b For structural assignments refer to Figure 5. 

A select list of species containing sulfur plus an additional heteroatom is given in Table III. These groups of compounds have been observed in coal derived products from various sources. To be able to make reasonable comparisons only data from bituminous coals are used. Possible structures for the formulae given in Table III are shown in Scheme I. It should be emphasized that further information is necessary to positively assign structures. The viability of these structural assignments will be discussed in the next three sections. 

The detection of linkages between monomeric units is a cumbersome process, dependent on the presence of key data points, and so other sources of information such as biosynthetic pathways are incorporated in a structural assignment. 

Tecleanone (55), the first o-aminobenzophenone to be isolated from a natural source, is a constituent of Diphasia klaineana, Teclea verdoomiana, and T. grandifolia. ° The structure assigned to tecleanone was based on the spectral data, fragmentation in the mass spectrometer into the ions (A) and (B) being particularly... 

McDowell and coworkers (15J studied the high resolution infrared spectrum of UF5 at ambient and low temperatures. This work was followed by a series of vibrational and electronic spectroscopic studies of matrix isolated UFg (16,17,18,19,20). In the first experiments, UFg deposited in Ar or CO matrices was vibrationally characterized by infrared spectroscopy and then exposed to broadband UV radiation at 10°K. In argon, photoreduction proceeded rapidly the 619 cirri UF5 infrared peak decreased in intensity while two new peaks grew in at 584 cirri anc 561 cirri. The new peaks were assigned to the expected UF5 photolysis product and a tentative C4V structure assignment was made. The wavelength dependence of the photoreduction was studied using a monochroma-tized UV source (1 kw Hg-Xe lamp, Schoeffel 6M-250 monochromator). The relative quantum efficiency of the UF5 dissociation per unit absorbance of UFg was found to be relatively constant in the allowed B-X absorption band (250-300 nm) (T7). Radiation in the... 

During the past year a variety of new guaianolides have been isolated from various plant sources and their structures assigned on the basis of spectroscopic data. These compounds include linichlorin-A (561), -B (562), and -C (563) Centaurea linifolia), aguerin-A (564) and -B (565) (Centaurea canariensis), ... 

Figure 9 In situ analysis of the pigment haemoventosin in the apothecia of a microlichen Haematomma ventosum using FT-LMMS. The structural assignment of the anions of major diagnostic interest is based on the high accuracy m/z data in Table 1. (Reprinted from Van Roy W, Mathey A, and Van Vaeck L (1996) In-situ analysis of lichen pigments by Fourier transform laser microprobe mass spectrometry with external ion source. Rapid Communications in Mass Spectrometry 10 562-572 Wiley.)...

Figure 11 Identification of the interaction products between the triethanolamine oleate additive of a lubricating emulsion and rolled aluminum. Top positive ion mass spectrum recorded using FT-LMMS with an external ion source. Bottom structural assignment of the ions of major diagnostic interest. The corresponding high accuracy miz data are listed in Table 2. The framed structures are indicative of the binding of the additive to aluminum. (Reprinted from Poels K, Van Vaeck L, Van Espen P, Terryn H, and Adams F (1996) Feasibility of Fourier transform laser microprobe mass spectrometry for the analysis of lubricating emulsions on rolled aluminum. Rapid Communications in Mass Spectrometry W 1351-1360 Wiley.)...

The ketonic alkaloid hypecorinine, C20H17O6N, Vmax 1690 and 1630 cm (5.92 and 6.14 fi) was obtained from several sources, including Corydalis incisa Pers. (Fumariaceae). The characteristic instability of the molecule toward acid was indicative of the presence of an aminoketal function. Lithium aluminum hydride reduction of hypecorinine gave rise to a pair of diastereomeric diols 5 and 6 identified as bicucullinediol and adlumidinediol, respectively. This chemical interrelation, coupled with the absence of hydroxyl absorption in the IR spectrum of the alkaloid confirmed the structure assigned ... 

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