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Absorption spectra of protein chromophores

Authors: M.A.L. Marques, A. Castro, and A. Rubio

Ref.: EXC!TiNG Summer School, organized by T. Andersen. Riksgränsen, Sweden, 22-30/6/2003 (2003)

Abstract: Not surprisingly, the theoretical understanding of biophysical processes is a very active field of research. In particular, there have been spectacular advances in the characterisation of structural and dynamical properties of complex biomolecules by a combination of quantum-mechanical and classical-molecular mechanics methods (QM-MM). However, and in spite of the large amount of experimental work in photo-active molecules, the theoretical description of the interaction of these molecules with external time-dependent fields is very much in its infancy. Photo-active molecules relevant for biology include retinal (responsible for the process of vision), the green fluorescent protein (GFP), chlorophyll, etc. On the other hand, time dependent density functional (TDDFT) theory has proved to be an invaluable tool for the calculation of excitation spectra of molecules. We will present a way to combined QM-MM methods (for the ground state) with TDDFT (for the description of the excited states) to calculate optical absorption spectra. Our first test case, the GFP, yielded remarkably good results. Very recent work on retinal and on the DNA basis will also be reviewed.

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