Theoretical study of indole: protonation, indolyl radical, tautomers of indole, and its interaction with water

Somers, Krf; Kryachko, Eugene S.; Ceulemans, Arnout

doi:10.1016/j.chemphys.2004.02.010

Cited by 50 publications

(51 citation statements)

References 51 publications

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“…These correspond to red shifts of 0.04 and 0.07 eV with respect to vertical transition energies calculated in the gas phase. 46 Somers and co-workers' results for the 1 L a state using a CHARMM force field and CHARMM point charges vary significantly depending on whether long-range interactions were included in the dynamics; small red shifts are observed with long-range electrostatics, whereas large blue shifts are observed with long-range electrostatics excluded. For this mutant and upon addition of explicit residues we observe that the TDDFT-calculated transitions red-shift, with the 1 L a state undergoing the largest shifts.…”

Section: Resultsmentioning

confidence: 99%

Modeling the Absorption Spectrum of Tryptophan in Proteins

et al. 2005

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We have applied time-dependent density functional theory (TDDFT) to study the valence π-π* excited states of the tryptophan chromophore in the environment of the proteins barnase and human serum albumin. The chromophore is represented by indole. Due to the approximate nature of TDDFT, in the gas phase the calculated vertical transition energies to the 1 L valence states are reordered with respect to experiment. The 1 L a state responds more than the 1 L b state to the local environment, described fully at the TDDFT level, and to bulk environment, described by a set of point charges. Nevertheless, the vertical transitions are readily identified. For human serum albumin, our calculations predict distinct spectral characteristics between structures with different tryptophan side chain torsion angles. The computational tractability of TDDFT relative to more accurate ab initio methods allows a large part of the surrounding protein environment (up to 100 atoms) to be explicitly included in the TDDFT calculations.

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Section: Resultsmentioning

confidence: 99%

Modeling the Absorption Spectrum of Tryptophan in Proteins

et al. 2005

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“…Hydroxy-indole has six carbon connecting isomers, i.e., there are six possible sites of substituting a hydrogen atom of indole by the OH radical group. The most stable, lower energy tautomer is 7-hydroxy indole (3) where the OH radical is bonded to C7 of benzene [29].…”

Section: Discussionmentioning

confidence: 99%

“…The oxyindole oxidation can give several products such as 2,4-, 2,5-, 2,6-and 2,7-oxyindoles [16]. The most stable, lower energy tautomer, is 2,7-oxyindoles [29].…”

Section: Differential Pulse Voltammetrymentioning

confidence: 98%

Pathways of Electrochemical Oxidation of Indolic Compounds

2011

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The electrochemical behaviour of indole and a group of indole-containing compounds with a substituent at the C3 position, indol-3-acetamide (IAM), tryptamine, gramine, indole acetic acid (IAA), indole propionic acid (IPA), indole butyric acid (IBA) and tryptophan, was investigated at a glassy carbon electrode, in order to determine their oxidation pathways. Indole undergoes one irreversible pH dependent oxidation, whereas the oxidation process of indole derivatives was more complex, a two step, the oxidation at C2 position on the pyrrole ring followed by the hydroxylation at the C7 position of the benzene moiety of indoles, irreversible pH dependent oxidation.

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“…It is a well-established fact that the benzene ring of indoles is less reactive than the pyrrole ring. Since all indole derivatives are substituted, the oxidation reaction taking place at the main peak (Ox 1 ) corresponds to the oxidation at nitrogen on the pyrrole ring 43,44 . The cyclic voltammograms of the indole library and model compounds demonstrated that the oxidation potential peak values were close to those of the nonsubstituted indole nucleus, but higher than those described for the antioxidant melatonin.…”

Section: Electrochemical Measurementsmentioning

confidence: 99%