Subsystem-Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies

• Published in: Chemphyschem Vol. 10; no. 18; pp. 3148 - 3173
• Main Author: Neugebauer, Johannes
• Format: Journal Article
• Language: English
• Published: Weinheim WILEY-VCH Verlag 21.12.2009; WILEY‐VCH Verlag; Wiley
• Subjects: ab initio calculations; Biological and medical sciences; density functional calculations; electronic structure; Energy Transfer; Fundamental and applied biological sciences. Psychology; Kinetics; Luminescent Proteins - chemistry; Molecular biophysics; Molecular Dynamics Simulation; Photochemistry. Photosynthesis. Bioluminescence; photophysics; Protein Conformation; Proteins - chemistry; Quantum Theory; Radiation-biomolecule interaction; Spectrum Analysis - methods; UV/Vis spectroscopy; Polarization; Theory; Biochemical compound; Strong interaction; Review; Complexes; UV/Vis spectroscopy; Mechanism; Protein; density functional calculations; Electronic structure; Density functional; ab initio calculations; Energy; Molecular assembly; Physical model; Environment; Calculation; photophysics; Electrostatics; Chromophore; Ultraviolet visible spectrometry
• ISSN: 1439-4235; 1439-7641; 1439-7641
• DOI: 10.1002/cphc.200900538

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. Pigment–pigment and pigment–environment interactions tune the optical properties of chromophores in biomolecular assemblies. Theoretical methods that exploit the subsystem structure of such systems (see graphic) in calculations of their spectra have made great progress during the past years. Recent developments and applications are reviewed herein.