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Mass Spectrometry in Natural Product Structure Elucidation

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Progress in the Chemistry of Organic Natural Products 100

Part of the book series: Progress in the Chemistry of Organic Natural Products ((POGRCHEM,volume 100))

Abstract

Starting in the sixties of the last century mass spectrometry has steadily gained in importance in natural products chemistry. Originally limited to electron ionization of molecules that can be vaporized un-decomposed in high vacuum, the introduction of alternate ionization techniques allows today the access to compounds with masses well over one million Daltons. In this review six classes of natural products will be presented where structural information can be obtained from the fragmentation patterns, considering also historical developments. Using the example of pentacyclic triterpenoids, it is shown how structural studies with electron ionization have been developed over the years. Vertebrate alkaloids cover a field where the structural studies mainly stem from the last twenty years relying also on electron ionization but in part introducing more recent techniques. The chapters on lipids and on carbohydrates demonstrate specifically how new ionization techniques have allowed the handling of involatile compounds and have extended the area of structural research step by step. The chapters covering peptides and nucleotides show the access to very high masses and to three-dimensional information of molecules. Fast computers with almost unlimited data storage capacities have made possible automated structural studies and the analysis of complex mixtures.

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Notes

  1. 1.

    McLafferty rearrangement (transfer of the C-15 H) of the 7-oxo compound with subsequent cleavage of the 12,13-bond (cf. 11c → g) would lead to an ion m/z 277).

  2. 2.

    Kindly provided by Prof. Dr. Sabira Begum, University of Karachi, Pakistan.

  3. 3.

    As an example for the danger possibly arising from relying on an isolated literature reference: for olean-18-ene-3-one (50) quotes the expected m/z 204 with 64% rel. int. and m/z 218 with 24%, while (91) quotes m/z 218 with 100% and not m/z 204.

  4. 4.

    “Ueberhaupt scheint es mir auch angemessen, die bis jetzt bekannten alkalischen Pflanzenstoffe nicht mit dem Namen Alkalien, sondern Alkaloide zu belegen, da sie doch in manchen Eigenschaften von den Alkalien sehr abweichen.” (Actually, it seems to me as adequate to designate the alkaline plant constituents known till now not as alkalis but rather as alkaloids as they differ much in several aspects from the alkalis) (102).

  5. 5.

    “Unter Alkaloiden im engeren Sinn verstehen wir dagegen Verbindungen mit heterocyklisch gebundenen Stickstoffatomen, mehr oder weniger stark ausgeprägtem basischem Charakter, ausgesprochener physiologischer Wirkung, kompliziertem molekularem Bau, die in Pflanzen gefunden werden, …” (Under alkaloids in a more restrictive sense we understand however compounds with heterocyclic bound nitrogen atoms, more or less pronounced basic character, explicit physiological activity, complicated molecular structure, which are found in plants, …) (103). This classical definition by Winterstein and Trier from 1910 was criticized by Pelletier in the introductory chapter of the first volume of the series Alkaloids: Chemical and Biological Perspectives (104). He offered a rather vague new definition—“An alkaloid is a cyclic organic compound containing nitrogen in a negative oxidation state which is of limited distribution among living organisms.”—and justified the wording as excluding compounds that should not be considered as alkaloids.

  6. 6.

    In a detailed GC/MS study it could be shown that alkaloids present in the skin of the Brazilian toad Melanophryniscus simplex were also to be found in the same relative portions in muscles, liver etc. (137 ).

  7. 7.

    Feeding on poisonous prey with the purpose to sequester toxic compounds for their own defense is spread over the entire animal kingdom (for examples, see Sect. 4.2). It is an ongoing field of interdisciplinary research (140) where mass spectrometry plays an important role (screening and identification, structural transformations, labeling studies, etc.).

  8. 8.

    In (119) under Supporting Information, with the exception of the steroidal alkaloids, all known amphibian alkaloids are listed, including samples for which the structures have not been established yet or are considered as tentative. The listing follows the shorthand designation (see above) and hence the molecular masses. The data comprise elemental formulas (for unknown structures based on high resolution MS measurements), diagnostic EI-MS fragments, GC and other characteristic data, and where known, assignment to a structural class, natural origin etc. It should be mentioned that 127 complete EI mass spectra of frog alkaloids can be found in (602).

  9. 9.

    A poisonous substance from toad skin glands was apparently first isolated by Phisalix and Betrand in 1893 (148) and named bufoténine (149). Jensen and Chen (150) described in 1932 several bufotenines, which they characterized as indole derivatives. The constitution of 22 was finally established 1934 by Wieland et al. (151).

  10. 10.

    For an enantioselective synthesis of the alkaloids cis-195A, (pumiliotoxin C) and trans-195A, see (161).

  11. 11.

    Dr. H.M. Garraffo, Bethesda, MD, private communication.

  12. 12.

    For syntheses of 5,8-disubstituted indolizidines, see (168, 169).

  13. 13.

    The 17β-hydroxy isomer of 55 allegedly (212) obtained (cf. (183)) from the Asian salamander Cryptobranchus maximus exists only as a synthesis product (209). For a total synthesis of samandarone (16-oxo analog of 55) see (210). For additional literature, see (671).

  14. 14.

    Californian garter snakes (Thamnophis sp.) can accumulate tetrodotoxin (49) especially in the liver and store it for prolonged periods of time. In this way the non-venomous snake becomes poisonous for its mainly avian predators. Tetrodotoxin is sequestered by eating newts (Taricha sirtalis) (see Sect. 4.1.2) (140, 223), whose skin contains the toxin. The snake has become resistant by changing the amino acid pattern of the muscular Na+ channels (224) in the area critical for the binding of tetrodotoxin.

    A second example constitutes the Asian snake Rhabdophis tigrinus, which collects in its nuchal glands dietary toad venoms (see Sect. 4.1.1.16) (225, 226).

    Another defense system of snakes consists of the ejection of an evil-smelling fluid from anal glands. GC/EI-MS analysis of the volatile components of the secretions of garter snakes (Thamnophis spp.) resulted in the identification of small (C2 to C5) carboxylic acids, (CH3)3 N, and 2-piperidone. The same compounds were also found in the secretions of species from other snake families (672). Analysis of the secretion of Dumaril’s ground boa (Acrantophis dumerili) (673, 674) yielded cholesterol, fatty acids, and their amides. Among the volatile compounds small carboxylic acids (C3 to C5) were identified by GC/EI-MS. Three compounds were tentatively classified as amines. The ion m/z 30 of high abundance accompanied by m/z 44 (20% rel. int.) suggests the presence of a -CH2-CH2-NH2 end group. The low abundance of all other ions would be in agreement with aliphatic amines (17), but the ions m/z 172, 186, and 200 considered as molecular ions would have to be [M + H]+ species. In the secretion of the western diamondback rattlesnake (Crotalus atrox) 1-O-monoalkylglycerols were found (676) and identified by the EI spectra of their trimethylsilyl and isopropylidene derivatives; cf. Sect. 5.2.1.

  15. 15.

    For example, exendin-3 and -4 with 39 amino acids (213, 214), helodermin with 35 amino acids (215), helospectin I and II with 38 and 37 amino acids, respectively (216), or helothermine containing approximately 220 amino acids (217). For mass spectrometric techniques used for the structure elucidation, see Sect. 7.2.1.

  16. 16.

    Ions m/z 73, 147, and 221 have been observed in GC column bleeding (239).

  17. 17.

    FWHM: full width half maximum (17), a term used to define mass spectral resolution.

  18. 18.

    [M–H]− comprises the main ion (nominal mass 703, exact mass 703.3667 Da) consisting of 12C, 1H, 14 N, 16O and 32S isotopes, and it is accompanied by a series of satellites containing heavier isotopes. The ions 2 mass units higher (705 Da) comprise a species containing 34S and several other species made up of combinations of 13C, 2H, 15 N, 17O, 18O, 33S, all of them differing somewhat in their exact masses. With sufficiently high resolution obtainable with an ICR instrument they can be separated. The signal representing the 34S-containing ion can be recognized by the exact mass difference between 32S and 34S (1.9958 Da) and its high intensity (4.4% of the intensity of the m/z 703 signal for each S atom present in the molecule; all the other m/z 705 signals amounting to about 1% or less). The observed intensity of 8.6% establishes the presence of two S atoms.

  19. 19.

    Platypus and Echidna (in German Schnabeltier and Ameisenigel) produce in crural glands connected to a spur on each hind limb toxic proteins of 4–6 kDa size (679–681), which in part resemble those of reptiles (682).

  20. 20.

    The lorises when threatened raise their arms and eject the content of brachial glands together with saliva. GC/MS analysis of the secretion has revealed the presence of a host of compounds, and LC/MS a single 17.6 kDa protein component consisting of two chains (7.8 and 9.8 kDa) linked by two disulfide bridges (720).

  21. 21.

    “It is a ravening beast, …, being touched it biteth deepe, and poisoneth deadly.” M.J. Dufton (657) in a historical review quotes from an English natural history text from 1607 enlarging then on the evil fame the shrew had in Britain and—probably introduced from there—in the USA. In the “Thierbuch” by Swiss Naturalist C. Gesner (1606) a similar statement can be found (“Ein klein fräsig/räubig Thier ist die Spitzmaus/eines unbarmhertzigen/trüglichen sins:.. und dañ so sie mag/so ertödtet sie mit ihrem giftigen biß” (A voraceous, rapaceous animal is the shrew, of a pitiless, deceptive mind: …and then if she wants she kills with her venomous bite) (662). In continental Europe, however, the fear seems to have been less pronounced: in a Swiss Natural History from 1809 there is nothing anymore from the deadly bite: “Es ist ein Irrthum, daß man sie für giftig hält, weil Hunde und Katzen sie nicht fressen, …” (It is an error to consider her as poisonous because dogs and cats don’t eat her) (661).

  22. 22.

    A few hints regarding the genesis of m/z 135 are: a compound lacking 3,4-methyl groups yields m/z 107, hence these methyl groups are not involved (710); compounds where both side chains contain double bonds conjugated with the furan ring yield the two ions arising from allylic cleavage (711, 717); small model compounds give no information (718); neither do analogous pyrrole compounds (718).

  23. 23.

    Kindly provided by Dr. P. Knechtle, Evolva SA, Reinach, Switzerland.

  24. 24.

    Post-source decay, this constitutes an ion fragmentation technique used with reflector-TOF instruments (17).

  25. 25.

    One must keep in mind that phosphate and sulfate residues have the same nominal mass and similar negative mass increments (-PO3H2 … 80.974, -SO3H … 80.965); see also (775).

  26. 26.

    Reference is given to (611). There are among other data major ions of an EI mass spectrum reported. The ion referred to as M+· (m/z 204) is 16 Da too low and the fragment ions correspond to those obtained from 22 (see Fig. 33). This would mean that the true M+· (m/z 220) is missing completely and only [M–O]+· is obtained, an unlikely proposition (generally not observed for N-oxides; even the EI mass spectrum of (CH3)3NO yields M+. (m/z 75) with 100% and [M−O]+· with 50% relative intensity. It seems more likely that the mass spectrum of 22 had been obtained.

  27. 27.

    For total syntheses, see (614).

  28. 28.

    In the Master’s thesis of Li-Ping Dai (612) bufogargarizanine D is designated as bufogargarizanine A. In addition to NMR data the ESI mass spectra of all three bufogargarizanines are reproduced, but they show besides [M + H]+ or [M–H]− signals of low to medium abundance a large number of peaks not belonging to the compounds in question.

  29. 29.

    Bufogargarizanines should not be confused with bufogargarizins, which are 19-nor-bufadienolides from the same animal (652).

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Acknowledgments

I wish to thank Mag. W. Dollhäubl and his team at Springer Verlag Wien for their competent help in preparing the figures in this contribution, as well as Prof. Dr. Sabira Begum, Karachi, Pakistan, Dr. H.M. Garaffo, Bethesda, MD, USA, Dr. P. Knechtle, Reinach, Switzerland, Dr. H. Münster, Bremen, Germany, and Dr. M. Schäfer, Köln Germany for spectral material.

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  1. Institut für Organische Chemie, Universität zu Köln, Greinstr. 4, 50939, Köln, Germany

    Herbert Budzikiewicz

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  1. College of Pharmacy, The Ohio State University, Columbus, Ohio, USA

    A. D. Kinghorn

  2. Institut für Organische Chemie, Johannes-Keppler-Universität Linz, Linz, Austria

    H. Falk

  3. Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan

    J. Kobayashi

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Budzikiewicz, H. (2015). Mass Spectrometry in Natural Product Structure Elucidation. In: Kinghorn, A., Falk, H., Kobayashi, J. (eds) Progress in the Chemistry of Organic Natural Products 100. Progress in the Chemistry of Organic Natural Products, vol 100. Springer, Cham. https://doi.org/10.1007/978-3-319-05275-5_2

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