Indole, aromaticity structure

To assess the trapping of biological nucleophiles, the pyrido[l,2-a]indole cyclopropyl quinone methide was generated in the presence of 5 -dGMP. The reaction afforded a mixture of phosphate adducts that could not be separated by reverse-phase chromatography (Fig. 7.16). The 13C-NMR spectrum of the purified mixture shown in Fig. 7.16 reveals that the pyrido [1,2-a] indole was the major product with trace amounts of azepino[l,2-a] indole present. Since the stereoelec-tronic effect favors either product, steric effects must dictate nucleophilic attack at the least hindered cyclopropane carbon to afford the pyrido[l,2-a]indole product. Both adducts were stable with elimination and aromatization not observed. In fact, the pyrido [1,2-a] indole precursor (structure shown in Scheme 7.14) to the pyrido [l,2-a]indole cyclopropyl quinone methide possesses cytotoxic and cytostatic properties not observed with the pyrrolo [1,2-a] indole precursor.47... 

Since tryptophan is recognized as a main constituent of plant proteins and as a common biogenetic precursor of the complex indole alkaloids, the wide occurrence of tryptamine derivatives in the plant kingdom is not unexpected. The presently known cases of these simple indole alkaloids have been ones in which a tryptamine unit formally appears as a slightly modified structure (e.g., by oxidation or methylation), as a cyclized form or a dimeric variation thereof, or as a modification which incorporates short carbon chains (e.g., C4, C2) or a simple aromatic structure (anthranilic acid) respectively. The great majority of the simple indole alkaloids are confined to the dicotyledon plants. 

The proton-decoupled 13C NMR spectrum of pergolide mesylate indicates the presence of twenty carbons, which are further identified as four non-protonated carbons, six methine carbons, and ten methyl and methylene carbons via a Distortionless Enhancement by Polarization Transfer (DEPT) spectrum. The eight aromatic and olefinic carbon resonances in the 134 ppm to 106 ppm region have chemical shifts consistent with an indole structure (2). The H NMR spectrum contains four aromatic proton resonances, from 6.88 to 7.22 ppm, whose chemical shifts are also indicative of an indole-type structure. The assignment of these carbon and proton resonances were confirmed with IH correlation spectroscopy (CDSY) and 3C-1H heteronuclear correlation spectroscopy (HETCORR). The UV spectrum also indicates the presence of an indole chromophore. 

The nonpolar amino acids (Figure 4.3a) include all those with alkyl chain R groups (alanine, valine, leucine, and isoleucine), as well as proline (with its unusual cyclic structure), methionine (one of the two sulfur-containing amino acids), and two aromatic amino acids, phenylalanine and tryptophan. Tryptophan is sometimes considered a borderline member of this group because it can interact favorably with water via the N-H moiety of the indole ring. Proline, strictly speaking, is not an amino acid but rather an a-imino acid. 

Besides the applications of the electrophilicity index mentioned in the review article [40], following recent applications and developments have been observed, including relationship between basicity and nucleophilicity [64], 3D-quantitative structure activity analysis [65], Quantitative Structure-Toxicity Relationship (QSTR) [66], redox potential [67,68], Woodward-Hoffmann rules [69], Michael-type reactions [70], Sn2 reactions [71], multiphilic descriptions [72], etc. Molecular systems include silylenes [73], heterocyclohexanones [74], pyrido-di-indoles [65], bipyridine [75], aromatic and heterocyclic sulfonamides [76], substituted nitrenes and phosphi-nidenes [77], first-row transition metal ions [67], triruthenium ring core structures [78], benzhydryl derivatives [79], multivalent superatoms [80], nitrobenzodifuroxan [70], dialkylpyridinium ions [81], dioxins [82], arsenosugars and thioarsenicals [83], dynamic properties of clusters and nanostructures [84], porphyrin compounds [85-87], and so on. 

Neither Fj nor F2 alone gave the characteristic fluorescence of fa and nicked fa in the presence of L-serine and pyridoxal phosphate. However, titration of a fixed amount of F2 with F2 gave rise to a fluorescence intensity 80-90% that of nicked fa at a stoichiometric ratio of Ft to F2. Moreover, both the excitation and emission spectra of the stoichiometric mixture were the same as for nicked fa. In addition, the same specific quenching of this fluorescence was shown in recombined Fj and F2 as in nicked fa. Further, the dissociation constants for L-serine and for indole were determined to be the same within experimental error for recombined Fj and F2, as for nicked fa. No significant differences were found between nicked fa and reconstituted Fj F2 in the intrinsic fluorescence of the aromatic residues, or in the sedimentation coefficients or the 200-250 nm CD spectra. From the foregoing independent lines of evidence, F2 and F2 combine to produce a structure very similar to that of nicked fa. 

Structural information on aromatic donor molecule binding was obtained initially by using H NMR relaxation measurements to give distances from the heme iron atom to protons of the bound molecule. For example, indole-3-propionic acid, a structural homologue of the plant hormone indole-3-acetic acid, was found to bind approximately 9-10 A from the heme iron atom and at a particular angle to the heme plane (234). The disadvantage of this method is that the orientation with respect to the polypeptide chain cannot be defined. Other donor molecules examined include 4-methylphenol (p-cresol) (235), 3-hydroxyphenol (resorcinol), 2-methoxy-4-methylphenol and benzhydroxamic acid (236), methyl 2-pyridyl sulfide and methylp-tolyl sulfide (237), and L-tyrosine and D-tyrosine (238). Distance constraints of between 8.4 and 12.0 A have been reported (235-238). Aromatic donor proton to heme iron distances of 6 A reported earlier for aminotriazole and 3-hydroxyphenol (resorcinol) are too short because of an inappropriate estimate of the molecular correlation time (239), a parameter required for the calculations. Distance information for a series of aromatic phenols and amines bound to Mn(III)-substituted HRP C has been published (240). 

Scheme 1. Principle of cyanine dye synthesis leading to trimethine (n = l), pentamethine (n = 2) and heptamethine (n = 3) chromophores. Structures comprising indolic subunits are usually named indocarbocyanine, indodicarbocyanine and indotricarbocyanine, respectively. Formic acid, malonic aldehyde, glutaconic aldehyde are used in their protected dianUide or orthoester form. They can be applied as substituted derivatives to introduce residues into the polymethine unit. The indolic substructure might bear further residues or annelated aromatic rings...

---