Structural Elucidations

Chemical interconversion to thalicarpine and application of these generalizations allow structural assignments for the phenolic analogs of thalicarpine. 

Thalicarpine can be selectively O-demethylated using sodium benzyl-selenolate in refluxing DMF to give the diphenol 

Progress in the chemistry of betacyanins depended on the development of efficient methods for their isolation and separation. Betalains often occur as complex mixtures and are easily decomposed during the purification steps, which render the isolation of larger amounts of material for structural studies difficult. It is therefore understandable that some of the compounds described during the 1960s need reinvestigation by modem techniques. 

The first separations of individual betacyanins were carried out by paper chromatography (55). The observation that betacyanins migrate on paper electrophoresis at pH 2 to 7 toward the anode was used for analyses of the betalain pigments from red beet (36,37) and other plants (38). This method was subsequently applied by two groups (3,4) for the isolation of crystalline betanin from a crude pigment preparation from red beet (39). 

A number of general methods have been developed for the structural elucidation of betacyanins. In almost all cases the betacyanins are hydrolyzed with 1 N HCl in order to identify the aglycone. Derivatives of betanidin (1) yield a mixture of 1 and isobetanidin (6) under these conditions, whereas isobetanidin derivatives yield only 6 (40). Betacyanins that are epimers at C-15 can be partially interconverted by treatment with dilute alkali under the exclusion of oxygen (25) or with 5% aqueous citric acid at room temperature (41). 

The position of the sugar residue in the dihydroindole portion can be determined by methylation of the pigment with diazomethane and subsequent alkaline degradation of the resulting neobetanin derivative. In the case of 5-0-glycosides, 5-hydroxy-6-methoxyindole-2-carboxylic acid is obtained, whereas the 6-O-glyco-sides yield 6-hydroxy-5-methoxyindole-2-carboxylic acid (47,48). The indole carboxylic acids are easily identified by TIjC. 

Most of the betalain pigments described in the 1960s have not been characterized by mass or NMR spectra. With FAB MS now at hand, the molecular ions of underivatized betalains can be easily determined, and the sensitivity of high-field NMR spectrometers allows the complete structural assignment, even of small samples. For the structural determination of oligosaccharide moieties, modem two-dimensional (2D) NMR techniques are now the method of choice. 

Canthin-6-one (1) has been isolated from 25 of the 36 species of plants in Table I and from cell cultures of Ailanthus altissima (13-16). Canthin-6-one is one of the most widely distributed alkaloids in plants. It has been reported (77) that 1 is contained in 9 of 33 species in the genus Rhododendron of the family Ericaceae of China. Readers are referred to Volume 8 (p. 249) of this treatise for its structure (5). 

Canthin-6-one N-oxide (9) has been isolated from the wood (18), root 

1 l-Hydroxycanthin-6-one (amarorine) C,4H8N2O2 323-325 Amaroria soulameoides (syn. Simaroubaceae 44,45 

1 l-Methoxycanthin-6-one (amoridine) C,5H,oN20j 237-238 Amaroria soulameoides Simaroubaceae 44 

8-hydroxycanthin-6-one (18), 10 was estimated to be the 1-hydroxyl derivative. Through direct comparison between methylated 10 and 1-methoxycanthin-6-one (11), structure 10 was confirmed. 

The mass spectroscopic fragmentation of phyllalbine gave essentially the same species as did atropine and other tropeines studied by Djerassi et al. (Safi) and controlled by the use of deuterated samples. This will be dealt with further in Section VI. 

The product (mp 134°) obtained on oxidation of valeroidine (III) with permanganate (9) was first formulated as a lactone (IV) on the basis of analytical figures, and then described later (10) as a cyclic carbonate (V) (see structure XLIV in Volume VI, p. 160) of norvaleroidine (VI). 

Recently it was subjected to spectroscopic examination (11) surprisingly, it has a strong band in the infrared at 3200 cm i, pointing to a hydroxyl in the NMR-spectrum it gives a proton signal at 8.05 S, 

The chloride (IX) on reaction with alkali, gave two isomeric diols, one being ecgoninol (XI) while the other was deduced by ring opening at C-3 to be presumably the 2(8-hydroxymethyl-3a-tropanol (XIII). The isomerization of this hydroxyl by alkali gave another tropanediol  

Acyl migration in N- and 0-acylnorpseudotropines (19) involves the boat conformation in the transition state. Its presence in the ground state was indicated in an early infrared study (20) by a different ratio in bonded to nonbonded hydroxyls in the two epimeric 3-tropanols. An 

Wheat pentosans were dehydrated to furfural with concentrated HC1, and the furfural was dissolved in dibutyl ether in preparation for GC (Folkes, 1980). This method is claimed to be specific, accurate, and precise for pentoses and pentosans (Folkes, 1980), because 5-hydroxymethylfurfural is not produced, as is the case in hexose decomposition. Previously, furfural was distilled and analyzed colorimetrically. Alkalization increases the yield of 1-, 2-, and 3-carbon, vapor-phase compounds at the expense of anhydro sugars and furans (Ponder and Richards, 1993). Hydrolysis-GC is adaptable to the estimation of DP (Morrison, 1975) applicability to carbohydrates is limited to oligomers with DP = 6 (Traitler et al., 1984). 

In preparative GC, each separated fragment or derivative passes through a nondestructive detector, or a minor portion of the effluent stream is diverted to the detector and the remainder collected. 

Supercritical fluid chromatography (SFC) is a GC method of analysis of compounds in systems where normal GC presents resolution difficulties (Lee and Markides, 1987). A supercritical fluid has properties at a critical temperature intermediate between a liquid and a gas. At and above this critical temperature, a gas cannot be compressed into a liquid, irrespective of the pressure, but it solvates solid matter as if it were a liquid. A supercritical fluid diffuses freely into and out of adsorbent pores with a minimum of resistance. A major advantage of SFC chromatography is its ability to effect separation of oligomers without derivatization. 

SFC-GC and flame ionization detection (Chester, 1984) were thought of with the idea of extending the size analytical capability, while simultaneously enhancing resolution and lowering the separation temperature of silyl ethers of corn syrup carbohydrates (Chester and Innis, 1986). 

Using the density equation of dispersed polysaccharides at concentrations obeying Raoult s law, t , may be obtained from Vt vs ct (Walter and Matias, 1989). When V vs ci is not linear, , must be stated at a given c,. Subsequent to 4 , determinations, configurational AS [Eq. (3.22)] were calculated for low-and high-methoxyl pectin. Low-methoxyl pectins were discovered to be less inclined to order themselves in an aqueous medium than high-methoxyl pectins (Walter, 1991). 

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Figure Bl.13.4. The inversion-recovery detennination of the carbon-13 spin-lattice relaxation rates in melezitose. (Reproduced by pemiission of Elsevier from Kowalewski J and Maler L 1997 Methods for Structure Elucidation by High-Resolution N R ed Gy Batta, K E Kover and Cs Szantay (Amsterdam Elsevier) pp 325-47.)...

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

After approaches to the solution of the major tasks in chemoinformatics have thus been outlined, these methods are put to work in specific applications. Some of these apphcations, such as structure elucidation on the basis of spectral information, reaction prediction, computer-assisted synthesis design or drug design, are presented in Chapter 10. 

Structure elucidation systems that utilized information from several spectroscopic techniques were initiated in the late 1960s at Toyohashi, Japan, and at the University of Arizona. 

Similarity search appears as an extremely useful tool for computer-aided structure elucidation as well as for molecular design. Here the similarity property principle is involved. This may be stated as ... 

Similarity search appears as an extremely useful tool for computer-aided structure elucidation as well as molecular design. 

Two systems will be introduced below on the one hand the DENDRAL system for automatic structure elucidation [25], which was one of the first expert systems on the other hand the EROS system [26], which can be used for simulating reactions. 

P7] N.A. B. Gray, Computer-Assisted Structure Elucidation, Wiley, New York, 1986. 

To identify the main methods and tools available for the computer prediction of spectra from the molecular structure, and for automatic structure elucidation from spectral data... 

Furthermore, the prediction of and NMR spectra is of great importance in systems for automatic structure elucidation. In many such systems, aU isomers with a given molecular formula are automatically produced by a structure generator, and are then ranked according to the similarity of the spectrum predicted for each isomer to the experimental spectrum. 

In many cases, structure elucidation with artificial neural networks is limited to backpropagation networks [113] and, is therefore performed in a supervised man-... 

M. S. Madison, K.-P. Schulz, A. A. Korytko, M. E. Munk, SESAMI an integrated desktop structure elucidation tool, Internet Journal of Chemistry, 1998, 1, 34. 

However, better use of spectral information for more rapid elucidation of the structure of a reaction product, or of a natural product that has just been isolated, requires the use of computer-assisted structure elucidation (CASE) systems. The CASE systems that exist now are far away from being routinely used by the bench chemist. More work has to go into their development. 

The other is the Organic Structure Elucidation work book created by Professor Bradley D Smith (Notre Dame)... 

WebSpectra includes 75 problems All the problems display the and C spectra several with DEPT or COSY enhancements A number include IR spectra Organic Structure Elucidation contains 64 problems all with and C NMR IR and mass spectra The exercises in both WebSpectra and Organic Structure Elucidation are graded according to difficulty Give them a try... 

FIGURE 13 27 These two welcome screens open the door to almost 150 spectroscopy problems The screens are used with permission of Professors Craig A Merlic (WebSpectra) and Bradley D Smith (Organic Structure Elucidation) See the text for the respective URLs... 

The antimalarial properties attributed to preparations from Dichroa febrifuga by the Chinese were confirmed about 1944 and two alkaloids, febrifugine (999) and isofebrifugine (1000), were isolated eventually. After difficult structural elucidations, syntheses of ( )-febrifugine followed it proved to be half as active as the natural material, itself far better than quinine, but the therapeutic index was disappointingly low (67HC(24-l)490). 

Echinomycin (131) has been shown to be an antitumor agent and to have antiviral and antibacterial properties. Its structure elucidation represents a triumph for and mass spectral studies (75JA2497). It has been demonstrated that echinomycin functions by inhibiting RNA synthesis in organisms such as Staphylococcus aureus. Echinomycin, levomycin and actinoleutin are members of the quinoxaline-peptide antibiotic family and all contain one or more quinoxaline rings (67MI21402). 

As a class the penicillins do not have a characteristic UV absorption spectrum. UV spectra did, however, play an important role in the structure elucidation of some of the penicillin degradation products during the early structure studies (B-49MI51104). 

The early investigations of the reactions of the penicillin class of compounds were largely of a degradative nature, and were primarily associated with structure elucidation. These have been discussed in detail (B-49MI51102) and some of the principal transformations are outlined in Schemes 2, 3 and 4 using benzylpenicillin as an example. Some of these reactions will be discussed in greater detail later in this section. 

The first step for any structure elucidation is the assignment of the frequencies (chemical shifts) of the protons and other NMR-active nuclei ( C, N). Although the frequencies of the nuclei in the magnetic field depend on the local electronic environment produced by the three-dimensional structure, a direct correlation to structure is very complicated. The application of chemical shift in structure calculation has been limited to final structure refinements, using empirical relations [14,15] for proton and chemical shifts and ab initio calculation for chemical shifts of certain residues [16]. 

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