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Interpretation of Nuclear Resonant Vibrational Spectra of Rubredoxin Using a Combined Quantum Mechanics and Molecular Mechanics Approach
Author(s) -
Paulsen Hauke,
Trautwein Alfred X.,
Wegner Patrick,
Schmidt Christian,
Chumakov Aleksandr I.,
Schünemann Volker
Publication year - 2011
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/cphc.201100595
Subject(s) - rubredoxin , spectral line , chemistry , molecular mechanics , molecular dynamics , molecular vibration , molecular physics , computational chemistry , physics , quantum mechanics , molecule , crystallography , organic chemistry
Nuclear resonant vibrational spectra of the reduced and oxidized form of a mutant of rubredoxin from Pyrococcus abyssii were measured and are compared with simulated spectra that were calculated by a combined quantum mechanics (QM) and molecular mechanics (MM) method. Density functional theory was used for the QM level. Calculations were performed for different models of rubredoxin. Realistic spectra were simulated with reduced models that include at least the iron center, the four cysteins coordinating it, and the residues connected to the cysteins together with a QM layer that comprises the first two coordination shells of the iron center. Larger QM layers did not lead to significant changes of the simulated spectra.