title: Subsystem-based theoretical spectroscopy of biomolecules and biomolecular assemblies.
abstract: The absorption properties of chromophores in biomolecular systems are subject to several fine-tuning mechanisms. Specific interactions with the surrounding protein environment often lead to significant changes in the excitation energies, but bulk dielectric effects can also play an important role. Moreover, strong excitonic interactions can occur in systems with several chromophores at close distances. For interpretation purposes, it is often desirable to distinguish different types of environmental effects, such as geometrical, electrostatic, polarization, and response (or differential polarization) effects. Methods that can be applied for theoretical analyses of such effects are reviewed herein, ranging from continuum and point-charge models to explicit quantum chemical subsystem methods for environmental effects. Connections to physical model theories are also outlined. Prototypical applications to optical spectra and excited states of fluorescent proteins, biomolecular photoreceptors, and photosynthetic protein complexes are discussed.
authors.affiliation: Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands. j.neugebauer@chem.leidenuniv.nl
authors.forename: Johannes
authors.initials: J
authors.lastname: Neugebauer
mesh_terms: D004735:Energy Transfer; D007700:Kinetics; D008164:Luminescent Proteins / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D013057:Spectrum Analysis / Q000379:methods*
chemical_list: D008164:Luminescent Proteins; D011506:Proteins