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Abstract:
In this work, multiscale QM/MM methods have been used to study spectroscopic properties of two metalloproteins, focusing on a consistent and nice comparison to experiment.
For the copper protein Azurin, first the influence of the QM subsystem size on geometrical properties was systematically studied using DFT methods. Here, a special focus was set on the central Cu-SCys distance, which required the inclusion of the second ligand shell around the copper to achieve agreement with experiment. EPR properties, mainly the ligand hyperfine coupling (HFC) were studied using DFT and post-DFT methods. In case of Azurin, the DFT methods tested here are not capable of describing the electronic structure of the copper center. Several approaches to the DLPNO-CCSD method for the calculation of ligand HFCs are discussed. It was shown, that DLPNO-CCSD when used with these approaches is capable of to be used in the context of transition metal centers in proteins and provides a certainly useful addition to the computational toolbox. Finally, these calculated values were used for simulation and comparison to the originally recorded spectra. This comparison adds another layer of description to the comparison between calculations and experiment.
In the second part, the di-iron active site of soluble Monooxygenase (sMMO) is studied. First, the sensitivity of the protocol established for model complexes is tested for different protonation states of the MMOHox intermediate. Secondly, different core motifs for the MMOHQ intermediate were investigated and compared to experiment. Aside from geometric analysis comparing to crystal structures and EXAFS, multiple spectroscopic properties were calculated: Mössbauer, X-ray absorption spectroscopy (XAS) and, in case of MMOHQ, Raman spectroscopy. Using these methods, a suggestion for the protonation states of the MMOHox core were made, followed by a detailed comparison of open and closed cores of MMOHQ. It was shown that the most plausible explanation for the experimental data is an open core for MMOHQ.
