Indole protonation, calculations

Electrophilic Aromatic Substitution. The Tt-excessive character of the pyrrole ring makes the indole ring susceptible to electrophilic attack. The reactivity is greater at the 3-position than at the 2-position. This reactivity pattern is suggested both by electron density distributions calculated by molecular orbital methods and by the relative energies of the intermediates for electrophilic substitution, as represented by the protonated stmctures (7a) and (7b). Stmcture (7b) is more favorable than (7a) because it retains the ben2enoid character of the carbocycHc ring (12). 

Reddy et al29 studied the molecule N6,N6-dimethyl-2,6-diaminobenz[cd]-indole, which is shown in Figure 6. The aim was to assess its suitability as an inhibitor of thymidylate synthase, an enzyme which is important in DNA biosynthesis. Three structures were investigated N1H, which is the amine form depicted, and N2H, the imine form, in anti- and syn-conformations, i.e. with the proton on Ni away from or towards the N2 proton, respectively. In the gas phase it was found that the order of stability is N1H > anti-N2H > syn-N2H, in a ratio of 73.1 20.3 6.6. Solvation then further favours the N1H form, and the ratios in solution are calculated to be 98.5 0.5 1.0. Unfortunately, the syn-N2H form is likely to be the conformation that binds most strongly to the enzyme, and so the calculations indicate that this molecule is unlikely to be a suitable inhibitor. 

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). 

HF calculations with the 6-31G(d) basis set were used to study the mechanism of the Michael addition (or Friedel-Crafts alkylation) reaction of indole with dimethyl alkylidenemalonate. This reaction proceeds through two transition states, TSi and TS2 in the first step, assumed to be rate determining, the new C-C bond is formed, whereas in the second step, proton transfer from indole to malonate occurs with the formation of the new C-H bond. The calculations show that the transfer and interaction of the 7r-electrons in the reactant molecules may play an important role in the cleavage of the original C=C bond and the formation of the new bonds (C-C and C-H) the electron transfer is believed to be the driving force for the reaction to occur. 

Electron density calculations by the LCAO MO method have been made for indole, pyridine and free and protonated pyrrolo[2,3- >]pyridine. The results are summarized in Scheme 1 (68RCR551). 

For benzo[b]furan and indole no such precise data are available, but it is possible to adduce some information from the various reactions described below. The positional reactivity orders for these molecules and also for benzo[b]thiophene, which have been calculated by various methods, are given in Table 8.1. In principle the ab initio calculations should be the more reliable, but neither the tt nor the (a + it) order is correct for benzo[6]thiophene, suggesting that these are incorrect for the other molecules also. The calculations using the STO-3G basis set certainly wrongly predict the site of most rapid protonation. Notably, only the Hiickel calculations give the correct order for benzo[b]thiophene and indeed they are usually the most reliable indicators for electrophilic aromatic substitution. 

The resolution of the data available affects the appearance of the maps dramatically - and thus what can be understood from them. Figure 29 shows the same map calculated at various resolutions at 3 A the side chain positions can be distinguished, but not their conformation except for very large residues, like the tryptophan in the figure. At 2.0 A, on the other hand, the side chain conformations are clearly identifiable and water molecules are seen, while at 1.1 A, both the benzene and indole rings have holes in them, and the positions of the protons on the side chains become visible. In addition, as was discussed above (Figure 15), the phases dominate the appearance of the electron density map, so even a high-resolution map with poor phases can be difficult to interpret. 

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