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Pathway for Mn-cluster oxidation by tyrosine-Z in the S2 state of photosystem II
No full textWater oxidation in photosynthetic organisms occurs through the five intermediate steps S0-S4 of the Kok cycle in the oxygen evolving complex of photosystem II (PSII). Along the catalytic cycle, four electrons are subsequently removed from the Mn4CaO5 core by the nearby tyrosine Tyr-Z, which is in turn oxidized by the chlorophyll special pair P680, the photo-induced primary donor in PSII. Recently, two Mn4CaO5 conformations, consistent with the S2 state (namely, S2 A and S2 B models) were suggested to exist, perhaps playing a different role within the S 2-to-S3 transition. Here we report multiscale ab initio density functional theory plus U simulations revealing that upon such oxidation the relative thermodynamic stability of the two previously proposed geometries is reversed, the S2 B state becoming the leading conformation. In this latter state a proton coupled electron transfer is spontaneously observed at ∼100 fs at room temperature dynamics. Upon oxidation, the Mn cluster, which is tightly electronically coupled along dynamics to the Tyr-Z tyrosyl group, releases a proton from the nearby W1 water molecule to the close Asp-61 on the femtosecond timescale, thus undergoing a conformational transition increasing the available space for the subsequent coordination of an additional water molecule. The results can help to rationalize previous spectroscopic experiments and confirm, for the first time to our knowledge, that the water-splitting reaction has to proceed through the S2 B conformation, providing the basis for a structural model of the S3 state
The S-2 State of the Oxygen-Evolving Complex of Photosystem II Explored by QM/MM Dynamics: Spin Surfaces and Metastable States Suggest a Reaction Path Towards the S-3 State
No full textSplit and polish: Quantum mechanics/molecular mechanics simulations reveal the role of spin surfaces, kinetics, and thermodynamics on the interconversion between two structural models of the {Mn4CaO5} cluster (see picture) in the S2 state of the water-splitting Kok's cycle in photosystem-II. The results account for the temperature, illumination, and procedure dependence of historical EPR experiments and suggest a detailed pathway for the S2 to S3 transition
QM/MM dynamics of a Peridinin model in triplet state in three prototypical solvents
Full text linkPeridinin (Per) is a carbonyl-containing carotenoid playing a key role in light harvesting and photoprotection in dinoflagellates. This carotenoid plays its photoprotective role by quenching the potentially dangerous 3Chl-a triplet state through the formation of the non-reactive 3Per triplet state through Dexter energy transfer mechanism. We have investigated by means of Quantum Mechanics/Molecular Mechanics dynamics simulations at room temperature the structural and dynamical properties of a Peridinin model system (PMS) in triplet state in three different solvents: cyclohexane, apolar/aprotic; acetonitrile, polar/aprotic; and methanol (MeOH), polar/protic. Our results of 3PMS in MeOH show that the lactonic carbonyl has a stronger tendency to accept hydrogen bonds compared to the corresponding singlet ground state (1PMS). This effect may play some so far overlooked role in Per-containing proteins (notably the water soluble Peridinin-Chlorophyll-Proteins – PCPs). The vibrational properties of the 3PMS dynamics in the three solvents have been analyzed by means of decomposition of the vibrational density of states in effective normal modes. The results show that the solute-solvent interactions can influence some vibrational bands of 3PMS; in particular, they are able to modulate the position of the lactonic C[dbnd]O stretching band. The situation is particularly evident in the case of MeOH, where the dynamics of the MeOH⋯O[dbnd]C hydrogen bond interactions can strongly influence the band position and shape. As vibrational spectroscopy (notably step-scan FTIR difference spectroscopy) has been largely used to investigate 3Per in PCPs, especially using the lactonic carbonyl stretching as a marker band to investigate the different photophysical role of each Per in the protein complex, this study represents an important step to understand the experimental spectra and to identify the Per(s) molecule(s) bearing the triplet in PCPs
Magnetic interactions in the catalyst used by nature to split water: a DFT plus U multiscale study on the Mn4CaO5 core in photosystem II
No full textAn important approach in the design of new environmentally friendly materials is represented by the study of analogous systems already existing in nature. In the search for new water splitting catalysts, the corresponding natural analogue is represented by the oxygen-evolving complex of photosystem II, which is a large membrane protein complex present in photosynthetic organisms. The understanding of the catalytic strategy of its active Mn4CaO5 core is important to unravel the mechanisms of water oxidation in photosynthesis and can serve as an inspiring model for the design of biomimetic catalysts based on largely non-toxic, earth abundant elements. The magnetic interactions between Mn ions are studied in the present work by means of DFT + U broken symmetry ab initio molecular dynamics within a quantum mechanics/molecular mechanics framework. The room temperature dynamics of two different structural models (i.e. with total high-spin and total low-spin ground states) was stable during the simulated time. We observed large fluctuations of the magnetic coupling constants calculated on both the structural models of the complex, causing occasionally instantaneous swapping of the ferromagnetic/antiferromagnetic coupling between the metal centers
Pathway for Mn-cluster oxidation by tyrosine-Z in the S-2 state of photosystem II
No full textWater oxidation in photosynthetic organisms occurs through the five intermediate steps S-0-S-4 of the Kok cycle in the oxygen evolving complex of photosystem II (PSII). Along the catalytic cycle, four electrons are subsequently removed from the Mn4CaO5 core by the nearby tyrosine Tyr-Z, which is in turn oxidized by the chlorophyll special pair P680, the photo-induced primary donor in PSII. Recently, two Mn4CaO5 conformations, consistent with the S-2 state (namely, S-2(A) and S-2(B) models) were suggested to exist, perhaps playing a different role within the S-2-to-S-3 transition. Here we report multiscale ab initio density functional theory plus U simulations revealing that upon such oxidation the relative thermodynamic stability of the two previously proposed geometries is reversed, the S-2(B) state becoming the leading conformation. In this latter state a proton coupled electron transfer is spontaneously observed at similar to 100 fs at room temperature dynamics. Upon oxidation, the Mn cluster, which is tightly electronically coupled along dynamics to the Tyr-Z tyrosyl group, releases a proton from the nearby W1 water molecule to the close Asp-61 on the femtosecond timescale, thus undergoing a conformational transition increasing the available space for the subsequent coordination of an additional water molecule. The results can help to rationalize previous spectroscopic experiments and confirm, for the first time to our knowledge, that the water-splitting reaction has to proceed through the S-2(B) conformation, providing the basis for a structural model of the S-3 state
Magnetic interactions in the catalyst used by nature to split water: a DFT plus U multiscale study on the Mn4CaO5 core in photosystem II
No full textAn important approach in the design of new environmentally friendly materials is represented by the study of analogous systems already existing in nature. In the search for new water splitting catalysts, the corresponding natural analogue is represented by the oxygen-evolving complex of photosystem II, which is a large membrane protein complex present in photosynthetic organisms. The understanding of the catalytic strategy of its active Mn4CaO5 core is important to unravel the mechanisms of water oxidation in photosynthesis and can serve as an inspiring model for the design of biomimetic catalysts based on largely non-toxic, earth abundant elements. The magnetic interactions between Mn ions are studied in the present work by means of DFT + U broken symmetry ab initio molecular dynamics within a quantum mechanics/molecular mechanics framework. The room temperature dynamics of two different structural models (i.e. with total high-spin and total low-spin ground states) was stable during the simulated time. We observed large fluctuations of the magnetic coupling constants calculated on both the structural models of the complex, causing occasionally instantaneous swapping of the ferromagnetic/antiferromagnetic coupling between the metal centers
The S-2 State of the Oxygen-Evolving Complex of Photosystem II Explored by QM/MM Dynamics: Spin Surfaces and Metastable States Suggest a Reaction Path Towards the S-3 State
No full textSplit and polish: Quantum mechanics/molecular mechanics simulations reveal the role of spin surfaces, kinetics, and thermodynamics on the interconversion between two structural models of the {Mn4CaO5} cluster (see picture) in the S2 state of the water-splitting Kok's cycle in photosystem-II. The results account for the temperature, illumination, and procedure dependence of historical EPR experiments and suggest a detailed pathway for the S2 to S3 transition. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Magnetic coupling constants and vibrational frequencies by extended broken symmetry approach with hybrid functionals
No full textThe description of the electronic structure and magnetic properties of multi-centers transition metal complexes, especially of mixed-valence compounds, still represents a challenge for density functional theory (DFT) methods. The energies and the geometries of the correctly symmetrized low-spin ground state are estimated using the Heisenberg-Dirac-van Vleck spin Hamiltonian within the extended broken symmetry method introduced by Marx and co-workers [Nair et al., J. Chem. Theory Comput. 4, 1174-1188 (2008)]. In the present work we extend the application of this technique, originally implemented using the DFT+U scheme, to the use of hybrid functionals, investigating the ground-state properties of di-iron and di-manganese compounds. The calculated magnetic coupling and vibrational properties of ferredoxin molecular models are in good agreements with experimental results and DFT+U calculations. Six different mixed-valence Mn(III)-Mn(IV) compounds have been extensively studied optimizing the geometry in low-spin, high-spin, and broken-symmetry states and with different functionals. The magnetic coupling constants calculated by the extended broken symmetry approach using B3LYP functional presents a remarkable agreement with the experimental results, revealing that the proposed methodology provides a consistent and accurate DFT approach to the electronic structure of multi-centers transition metal complexes. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4752398
Mechanism of Water Delivery to the Active Site of Photosystem II along the S(2) to S(3) Transition
Full text linkThe two water molecules serving as substrate for the oxygen evolution in Photosystem II are already bound in the S-2 state of the Kok-Joliot's cycle. Nevertheless, an additional water molecule is supposed to bind the duster during the transition between the S-2 and S-3 states, which has been recently revealed to have the Mn4CaO5 catalytic cluster arranged in an open cubane fashion. In this Letter, by means of ab initio calculations, we investigated the possible pathways for the binding of the upcoming water molecule. Upon the four different possibilities checked in our calculations, the binding of the crystallographic water molecule, originally located nearby the Cl- binding site, showed the lowest activation energy barrier. Our findings therefore support the view in which the W2 hydroxyl group and the O5 oxygen act as substrates for the oxygen evolution. Within this framework the role of the open and closed Mn4CaO5 conformers is clarified as well as the exact mechanistic events occurring along the S-2 to S-3 transition
Characterization of the Sr2+- and Cd2+-Substituted Oxygen-Evolving Complex of Photosystem II by Quantum Mechanics/Molecular Mechanics Calculations
No full textThe Mn4CaO5 cluster in the oxygen-evolving complex is the catalytic core of the Photosystem II (PSII) enzyme, responsible for the water splitting reaction in oxygenic photosynthesis. The role of the redox-inactive ion in the cluster has not yet been fully clarified, although several experimental data are available on Ca2+-depleted and Ca2+-substituted PSII complexes, indicating Sr2+-substituted PSII as the only modification that preserves oxygen evolution. In this work, we investigated the structural and electronic properties of the PSII catalytic core with Ca2+ replaced with Sr2+ and Cd2+ in the S2 state of the Kok-Joliot cycle by means of density functional theory and ab initio molecular dynamics based on a quantum mechanics/molecular mechanics approach. Our calculations do not reveal significant differences between the substituted and wild-type systems in terms of geometries, thermodynamics, and kinetics of two previously identified intermediate states along the S2 to S3 transition, namely, the open cubane S2A and closed cubane S2B conformers. Conversely, our calculations show different pKa values for the water molecule bound to the three investigated heterocations. Specifically, for Cd-substituted PSII, the pKa value is 5.3 units smaller than the respective value in wild type Ca-PSII. On the basis of our results, we conclude that, assuming all the cations sharing the same binding site, the induced difference in the acidity of the binding pocket might influence the hydrogen bonding network and the redox levels to prevent the further evolution of the cycle toward the S3 state. © 2015 American Chemical Society
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