Abstract
The recently developed 3-FDE method (Jacob and Visscher, 2008) combines ideas from the Molecular Fractionation with Conjugate Caps (MFCC) method (Zhang and Zhang, 2003) with Frozen Density Embedding (FDE) (Wesołowski and Warshel, 1993) and is thus able to produce fully quantum-chemical electron densities of entire proteins. In contrast to the original FDE method, 3-FDE facilitates a fragmentation into covalently bound subunits. We apply the method for the first time to the calculation of excitation energies, where we use the Fenna–Matthews–Olson (FMO) pigment–protein complex as a test case. Several technical and conceptual parameters for the preparation stages are tested and a robust protocol for this type of embedding is established. We present calculations of excitation energies of the individual pigments (site energies) under the influence of full protein densities obtained with different settings and compare them to the results from a simple point charge model. Our results indicate that 3-FDE is a well-suited method for the description of excitation energies within density-based embedding.
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