Distinguishing Features of Indolyl Radical and Radical Cation:  Implications for Tryptophan Radical Studies

Abstract

Tryptophan radicals or radical cations, currently believed to participate in electron transfer in cytochrome c peroxidase, DNA photolyase, galactose oxidase, and perhaps ribonucleotide reductase, are becoming increasingly conspicuous in proteins. Density-functional quantum chemical calculations for the indolyl radical (Ind • ) and radical cation (IndH •+ ) are reported to aid the distinction between the tryptophan radical (Trp • ) and the tryptophan radical cation (TrpH •+ ). For this evaluation of indole and the indolyl radicals, two densityfunctional methods were compared: the local spin density exchange functional of Slater combined with the local correlation energy expression of Vosko, Wilk, and Nusair (SVWN) and Becke's gradient-corrected exchange functional combined with Lee, Yang, and Parr's gradient-corrected correlation functional (BLYP). Both were employed with a 6-31G(d) basis set. In addition to providing molecular geometries, atomic spin densities, and approximate isotropic hyperfine coupling constants for modeling EPR and ENDOR spectra, results imply that (a) both Ind • and IndH •+ are π radicals with large spin density on N1 (see 1), so the observation of 14 N or 15 N hyperfine interactions alone is not sufficient to distinguish Trp • from TrpH •+ , (b) the different spin polarizations at C2 of Ind • and IndH •+ should form the basis for designing experiments to distinguish Trp • from TrpH •+ , (c) the large shift of the C2-C3 stretching mode of indole by approximately -200 cm -1 in Ind • may be useful to identify Trp • , and (d) analysis of the angular dependence of hyperfine interactions between the β-methylene protons of Trp • and the large spin density at C3, calculated for both Ind • and IndH •+ , may yield the orientations of Trp • side chains in proteins.

N-Substituted indole-3-thiolate [4Fe–4S] clusters with a unique and tunable combination of spectral and redox properties

“…The fact that both the NH and H2 protons are shifted to lower frequencies by contact interactions indicates the presence of same-sign spin densities at positions 1 and 2 of the indole-3-thiolate ligand. An analogous spin distribution has been found in the indole radical cation, [19] in contrast to thiophenolate-based systems, in which neighboring hydrogen atoms generally display opposite-sign contact shifts [18].…”

Unexpected Reaction Promoted by NH+···O=Mo Hydrogen Bonds in Nonpolar Solvents

“…On the other hand, the one-electron oxidation of indole (IndH) to radical cation (IndH ·+ ) or neutral indoyl radical (Ind · ) with release of H + has been reported. [48] Because the pK a of the TrpH ·+ radical cation is 4.3, it easily releases a proton to form neutral Trp · radical. [49] Thus, the redox potential of tryptophan is dependent on the pH of the aqueous media.…”

Ditryptophan Cross-Links as Novel Products of Protein Oxidation

“…49 Additionally, a C-N bond was more consistent with a higher susceptibility of the cross-link to cleave under the MS/MS conditions than a C-C bond. This study provided the first clear evidence for the formation of a Trp-Trp cross-link in a protein by radical mechanisms, although the structure of the dimer was hypothesized, not characterized.…”

“…49 Therefore, radical dimerization can potentially occur at all of these sites, some of which resulting in different stereoisomers. Indeed, the reaction of N-acetyl-L-tryptophan amide with NO 2…”