title: Vibrational fingerprints of the Mn4CaO5 cluster in Photosystem II by mixed quantum-classical molecular dynamics.
abstract: A detailed knowledge of the structures of the catalytic steps along the Kok-Joliot cycle of Photosystem II may help to understand the strategies adopted by this unique enzyme to achieve water oxidation. Vibrational spectroscopy has probed in the last decades the intermediate states of the catalytic cycle, although the interpretation of the data turned out to be often problematic. In the present work we use QM/MM molecular dynamics on the S2 state to obtain the vibrational density of states at room temperature. To help the interpretation of the computational and experimental data we propose a decomposition of the Mn4CaO5 moiety into five separate parts, composed by "diamond" motifs involving four atoms. The spectral signatures arising from this analysis can be easily interpreted to assign experimentally known bands to specific molecular motions. In particular, we focused in the low frequency region of the vibrational spectrum of the S2 state. We can therefore identify the observed bands around 600-620cm(-1) as characteristic for the stretching vibrations involving Mn1-O1-Mn2 or Mn3-O5 moieties.
authors.affiliation: Dept. of Physical and Chemical Science, University of L'Aquila, via Vetoio Coppito, 67100 L'Aquila, Italy. Electronic address: daniele.bovi@roma1.infn.it.
authors.forename: Daniele
authors.initials: D
authors.lastname: Bovi
authors.affiliation: Dept. of Chemistry, University of Rome "La Sapienza", P.le Aldo Moro, 5, 00185 Roma, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Capone
authors.affiliation: Dept. of Physical and Chemical Science, University of L'Aquila, via Vetoio Coppito, 67100 L'Aquila, Italy; Present address: Lab. of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
authors.forename: Daniele
authors.initials: D
authors.lastname: Narzi
authors.affiliation: Dept. of Physical and Chemical Science, University of L'Aquila, via Vetoio Coppito, 67100 L'Aquila, Italy. Electronic address: leonardo.guidoni@univaq.it.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Guidoni
mesh_terms: D002118:Calcium / Q000378:metabolism*; D002384:Catalysis; D006860:Hydrogen Bonding; D008345:Manganese / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D010084:Oxidation-Reduction; D010100:Oxygen / Q000378:metabolism*; D045332:Photosystem II Protein Complex / Q000378:metabolism*; D011789:Quantum Theory; D014732:Vibration; D014867:Water / Q000378:metabolism
chemical_list: D045332:Photosystem II Protein Complex; D014867:Water; D008345:Manganese; D010100:Oxygen; D002118:Calcium
keywords: Density functional theory; FTIR; Infrared spectra; Photosystem II; VDOS