The challenge of predicting optical properties of biomolecules: What can we learn from time-dependent density-functional theory?

Abstract

The suitability of the time-dependent density-functional theory (TDDFT) approach for the theoretical study of the optical properties of biomolecules is demonstrated by several examples. We critically discuss the limitations of available TDDFT implementations to address some of the present open questions in the description of the excited-state dynamics of biological complexes. The key objective of the present work is to address the performance of TDDFT in the linear response regime of the bio-molecular systems to the visible or near UV radiation - measured by, e.g. optical absorption or optical dichroism spectra. Although these spectra are essentially determined by the electronic degrees of freedom of small, optically active regions within the usually large biological systems, they can also be strongly influenced by environment effects (solvent, hosting protein, temperature, etc.). Moreover, many key biological processes consist of photo-induced dynamics (photoisomerisation, etc.), and their description requires a coupled treatment of electronic and nuclear degrees of freedom. We illustrate these aspects with a selection of paradigmatic biomolecular systems: chromophores in fluorescent proteins, porphyrins, DNA basis, the azobenzene dye, etc. To cite this article: A. Castro et al., C. R. Physique 10 (2009). © 2008

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

“…The popular linear-response time-dependent DFT (TDDFT) method provides accurate excitation energies at a much lower cost than ab initio correlation calculations. [11][12][13] However, a number of problematic cases exists, where today's functionals are not able to provide accurate excitation energies. 2,5,[14][15][16][17][18] Thus, alternative methods to assess the accuracy of the TDDFT calculations on large molecules are needed.…”

A new time dependent density functional algorithm for large systems and plasmons in metal clusters

“…This scheme was introduced in the seminal work of Yabana and Bertsch 6 and is now implemented usually over real space grids, like in the OCTOPUS program, 7 which has been recently applied to study the photoabsorption of large biomolecules 8 and large metal clusters, clusters up to 147 atoms 9 and 263 atoms. 10 The second one consists in a superoperator formulation of the TDDFT, which allows the calculation of the dynamical polarizability by means of a very efficient Lanczos method, implemented with plane waves basis set; 11 it has been applied to systems like C 60 , C 70 , zinc tetraphenylporphyrin, and chlorophyll a.…”

Applications of large-scale density functional theory in biology

“…Nevertheless, these come in several relevant forms: TDDFT can be performed in a real-time formalism [166], which explicitly propagates time to study dynamical processes, or it can be performed in the linear-response framework [167], whereby the dynamical response of a system to an excitation at a specific frequency is considered, so as to find the energies of specific excitations. Both approaches have found application within the field of modelling small-scale biological molecules such as individual DNA bases and base-pairs [168], structures such as porphyrin rings [169], and chromophores embedded in protein environments such as those found in pigmentprotein complexes and fluorescent proteins [170]. Castro et al have provided a review of theory and applications of TDDFT to biomolecules up to 2009 [169].…”

“…Both approaches have found application within the field of modelling small-scale biological molecules such as individual DNA bases and base-pairs [168], structures such as porphyrin rings [169], and chromophores embedded in protein environments such as those found in pigmentprotein complexes and fluorescent proteins [170]. Castro et al have provided a review of theory and applications of TDDFT to biomolecules up to 2009 [169].…”