Dataset Information

Prediction of high-valent iron K-edge absorption spectra by time-dependent density functional theory.

ABSTRACT: In recent years, a number of high-valent iron intermediates have been identified as reactive species in iron-containing metalloproteins. Inspired by the interest in these highly reactive species, chemists have synthesized Fe(IV) and Fe(V) model complexes with terminal oxo or nitrido groups, as well as a rare example of an Fe(VI)-nitrido species. In all these cases, X-ray absorption spectroscopy has played a key role in the identification and characterization of these species, with both the energy and intensity of the pre-edge features providing spectroscopic signatures for both the oxidation state and the local site geometry. Here we build on a time-dependent DFT methodology for the prediction of Fe K- pre-edge features, previously applied to ferrous and ferric complexes, and extend it to a range of Fe(IV), Fe(V) and Fe(VI) complexes. The contributions of oxidation state, coordination environment and spin state to the spectral features are discussed. These methods are then extended to calculate the spectra of the heme active site of P450 Compound II and the non-heme active site of TauD. The potential for using these methods in a predictive manner is highlighted.

SUBMITTER: Chandrasekaran P

PROVIDER: S-EPMC3242413 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Prediction of high-valent iron K-edge absorption spectra by time-dependent density functional theory.

Chandrasekaran P P Stieber S Chantal E SC Collins Terrence J TJ Que Lawrence L Neese Frank F DeBeer Serena S

Dalton transactions (Cambridge, England : 2003) 20110929 42

In recent years, a number of high-valent iron intermediates have been identified as reactive species in iron-containing metalloproteins. Inspired by the interest in these highly reactive species, chemists have synthesized Fe(IV) and Fe(V) model complexes with terminal oxo or nitrido groups, as well as a rare example of an Fe(VI)-nitrido species. In all these cases, X-ray absorption spectroscopy has played a key role in the identification and characterization of these species, with both the energ ...[more]

PMID: 21956429

Similar Datasets

Project description:A detailed understanding and interpretation of absorption spectra of molecular systems, especially in condensed phases, requires computational models that allow their structural and electronic features to be connected to the observed macroscopic spectra. This work is focused on modeling the electronic absorption spectrum of a fluorescent probe, namely, the 9-(4-((bis(2-((2-(ethylthio)ethyl)thio)ethyl)amino)methyl)phenyl)-6-(pyrrolidin-1-yl)-3H-xanthen-3-one molecule, depicted by a combined classical-quantum chemical approach. Particularly, first classical molecular dynamics (MD) has been used to explore the configurational space, and next, the absorption spectrum has been reconstructed by averaging the results of time-dependent density functional theory (TD-DFT) calculations performed on equispaced molecular conformations extracted from MD to properly sample the configurational space explored at finite temperature. To verify the effect of molecular conformation on the spectral profile, the generated electronic absorption spectra were compared with those obtained considering a single structure corresponding to the optimized one, an approach also referred to as static. This comparison allows one to highlight a sizable though small shift between the maxima of the corresponding reconstructed absorption spectra, highlighting the importance of conformational sampling in the case of this rather flexible molecule. Four different exchange and correlation functionals (PBE, BLYP, PBE0, B3LYP) were considered to compute vertical transition via TD-DFT calculations. From the results obtained in gas and in condensed, here solution, phases, it appears that the magnitude of the shift is actually more affected by the phase in which the system is found than by the functional used. This fact underlines the central importance of conformational mobility, that is flexibility, of this molecule. From a more quantitative point of view, a comparison with available experimental data shows that hybrid functionals, such as PBE0 and B3LYP, enable one to faithfully reproduce the observed absorption maxima.

Dataset Information

Prediction of high-valent iron K-edge absorption spectra by time-dependent density functional theory.

Publications

Prediction of high-valent iron K-edge absorption spectra by time-dependent density functional theory.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets