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Excitation dynamics in Phycoerythrin 545: modeling of steady-state spectra and transient absorption with modified Redfield theory.

ABSTRACT: We model the spectra and excitation dynamics in the phycobiliprotein antenna complex PE545 isolated from the unicellular photosynthetic cryptophyte algae Rhodomonas CS24. The excitonic couplings between the eight bilins are calculated using the CIS/6-31G method. The site energies are extracted from a simultaneous fit of the absorption, circular dichroism, fluorescence, and excitation anisotropy spectra together with the transient absorption kinetics using the modified Redfield approach. Quantitative fit of the data enables us to assign the eight exciton components of the spectra and build up the energy transfer picture including pathways and timescales of energy relaxation, thus allowing a visualization of excitation dynamics within the complex.

SUBMITTER: Novoderezhkin VI

PROVIDER: S-EPMC2905105 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature

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Excitation dynamics in Phycoerythrin 545: modeling of steady-state spectra and transient absorption with modified Redfield theory.

Novoderezhkin Vladimir I VI Doust Alexander B AB Curutchet Carles C Scholes Gregory D GD van Grondelle Rienk R

Biophysical journal 20100701 2

We model the spectra and excitation dynamics in the phycobiliprotein antenna complex PE545 isolated from the unicellular photosynthetic cryptophyte algae Rhodomonas CS24. The excitonic couplings between the eight bilins are calculated using the CIS/6-31G method. The site energies are extracted from a simultaneous fit of the absorption, circular dichroism, fluorescence, and excitation anisotropy spectra together with the transient absorption kinetics using the modified Redfield approach. Quantita ...[more]

PMID: 20643051

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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

Excitation dynamics in Phycoerythrin 545: modeling of steady-state spectra and transient absorption with modified Redfield theory.

Publications

Excitation dynamics in Phycoerythrin 545: modeling of steady-state spectra and transient absorption with modified Redfield theory.

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