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Energy Research

Molecular dynamics simulations of Photosystem II in membrane environment: The role of the dynamic in the PSII complex

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Photosystem II (PSII) is a homodimeric protein-cofactor complex embedded in the photosynthetic thylakoid membrane where it acts as a water: plastoquinone oxidoreductase, thus catalyzing the water splitting process [1]. PSII can capture and convert the sunlight-derived energy into chemical energy by simultaneously reducing plastoquinone molecules and oxidizing water molecules with the subsequent generation of molecular oxygen and a proton gradient across the membrane. Investigation of the molecular basis behind the PSII function is mandatory in order to reproduce artificially the photosynthetic process and ultimately to be able to convert solar energy into chemical energy close to the thermodynamic efficiency. The (low-resolution) x-ray structures of PSII solved in the last decade [1,2] as well as several spectroscopy and computational studies performed on PSII [3-5] allowed to build reasonable models describing the PSII function. However, the molecular mechanism behind the water splitting process still remains largely elusive and matter of debate. The last x-ray structure solved in 2011 by Umena et al. at a resolution of 1.9 A revealed for the first time a detailed structure of the catalytic center of water splitting [6]. We study by MD simulations the dynamical properties of the full PSII complex in a membrane environment after developing the force-field of all cofactors and lipids present in the structure solved by Umena et. al. On the basis of this setup we also perform QM/MM molecular dynamics simulations of the manganese cluster to investigate the effect of the protein environment on its structural properties and on the surrounding protonation pattern.



[1] A. Guskov et al. Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride. Nat. Struct. Mol. Biol. 16: 334-342 (2009) 

[2] J. Kern & G. Renger. Photosystem II: Structure and mechanism of the water:plastoquinone oxidoreductase. Photosynth. Res. 94: 183-202 (2007)

[3] A. Haddy. EPR spectroscopy of the manganese cluster of photosystem II. Photosynth. Res. 92: 357-368 (2007)

[4] P. Gatt et al. Application of computational chemistry to understanding the structure and mechanism of the Mn catalytic site in photosystem II - A review. J. Photochem. Photobiol. B Biol. 104: 80-93 (2011)

[5] P.E.M. Siegbahn. Recent theoretical studies of water oxidation in photosystem II. J. Photochem. Photobiol. B Biol. 104: 94-99 (2011)

[6] Y. Umena et al. Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 A. Nature 473: 55-61 (2011)



Transition metal complexes: the role of ligand in the polymerization of olefins and diolefins, experimental studies and theoretical approach

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In the last years transition metal complexes have attracted much interest in the processes of stereospecific polymerization. Polymers with different microstructures (cis-1,4; 1,2; mixed cis-1,4/ 1,2; 1,2; 3,4) and different tacticity (iso- or syndiotactic) [1], [2] were obtained from diolefins (1,3- butadiene, isoprene, 1,3-pentadienes, 1,3-hexadienes) and olefins depending on catalyst used; this means that catalyst structure (metal, type of ligand) strongly affect chemo- and stereoselectivity. The mayor effects of the ligand substitution on the catalysis have been recently reviewed by Ricci et al. [3], [4]. In the present contribution we study several catalytic complexes by quantum chemistry technique based on Density Functional Theory and ab initio molecular dynamics. Preliminary calculations on the optimized structures and the substrate binding energies may help to rationalize the experimental evidences.


[1] B. Pirozzi, R. Napolitano, G. Giusto, S. Esposito and G. Ricci, Macromolecules, 40 (2007) 8962.

[2] B. Pirozzi, R. Napolitano, V. Petraccone and S. Esposito, Macromol. Rapid Commun., 24 (2003) 392.

[3] G. Ricci, A. Sommazzi, F. Masi, M. Ricci, A. Boglia and G. Leone, Coordination Chemistry Reviews, 254 (2010) 661.

[4] G. Ricci, G. Leone, F. Masi and A. Sommazzi, Ferrocene: Compounds, Properties and Applications, Elisabeth S. Phillips Editors (2011) 273.


Artificial Photosynthesis

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Photosynthetic processes occurring in biological systems are designed to capture sunlight very efficiently and convert it into chemical energy, that is, organic molecules. Sunlight is indeed the only renewable and carbon-neutral energy source of sufficient scale to replace fossil fuels and satisfy the rising global energy demand. The success of photosyntesis depends upon the fact that the needed materials (sunlight, water and, possibly, carbon dioxide) are available in almost unlimited amounts[1,2]. The splitting of water by sunlight into oxygen and hydrogen is regarded as a key step of the photsyntetic processes. Molecular oxygen is released into the atmosphere; the hydrogen is not normally released but it is combined instead with carbon dioxide to make various kinds of organic molecule. In biological systems, water oxidation is catalyzed by a pentanuclear MnCa complex bound to aminoacid residues of photosystem II (PSII), which is characterized by a compact metal-oxocore with several di-?-oxo bridges between Mn ions. Large-scale technological production of molecular hydrogen (or other fuels) from water requires synthetic water-oxidation catalysts that are (i) similarly efficient as the photosynthetic Mn complex and (ii) based on inexpensive and abundant materials [1,2].



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