Evolution from S3 to S4 States of the Oxygen-Evolving Complex in Photosystem†II Monitored by Quantum Mechanics/Molecular Mechanics (QM/MM) Dynamics.

Water oxidation in the early steps of natural photosynthesis is fulfilled by photosystem II, which is a protein complex embedded in the thylakoid membrane inside chloroplasts. The water oxidation reaction occurs in the catalytic core of photosystem II, which consists of a Mn4Ca metal cluster, at which, after the accumulation of four oxidising equivalents through five steps (S0-S4) of the Kok-Joliot cycle, two water molecules are split into electrons, protons, and molecular oxygen. In recent years, by combining experimental and theoretical approaches, new insights have been achieved into the structural and electronic properties of different steps of the catalytic cycle. Nevertheless, the exact catalytic mechanism, especially concerning the final stages of the cycle, remains elusive and greatly debated. Herein, by means of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, from the structural, electronic, and magnetic points of view, the S3 state before and upon oxidation has been characterised. In contrast with the S2 state, the oxidation of the S3 state is not followed by a spontaneous proton-coupled electron-transfer event. Nevertheless, upon modelling the reduction of the tyrosine residue in photosystem II (TyrZ ) and the protonation of Asp61, spontaneous proton transfer occurs, leading to the deprotonation of an oxygen atom bound to Mn1; thus making it available for O-O bond formation.

Effects of Static Correlation between Spin Centers in Multicenter Transition Metal Complexes.

Multicenter transition metal complexes are the key moieties of many processes in chemistry, biochemistry, and materials science such as in the active sites of enzymes, molecular catalysts, and biological electron carriers. Their electronic structure, often characterized by high-spin-polarized metal sites, is a challenge for theoretical chemists because of their high degree of dynamical and static correlation. Static correlation is necessary both for the appropriate description of the metal-ligand bonding and for a correct description of the multideterminant character arising from the magnetic interactions between spin centers. Density functional theory (DFT) is usually applied using a single-determinant broken-symmetry state that is lacking the correct spin symmetry when the ground state has total low-spin character. To alleviate this drawback, we use the extended broken-symmetry (EBS) approach to derive approximate ground-state energies and, for the first time, forces for the correctly symmetric ground state of an arbitrary number of spin centers within the framework of the Heisenberg-Dirac-van Vleck Hamiltonian. Remarkably, the proposed procedure supplies relaxed geometries that are fully consistent with the calculated J-coupling constants. We apply the method to investigate the relaxed geometrical structure of the low-spin ground state of iron-sulfur clusters with two, three, and four iron centers. We observed significant differences in both geometrical parameters and coupling constant J between the symmetrized ground state, the high-spin, and the broken-symmetry optimized structures. These changes are often comparable with the differences observed by using different functionals, and the use of EBS always improves the description of the studied systems. It will be therefore important to include it in any DFT attempt to quantitatively describe multicenter transition metal complexes in the future.

A Spotlight on the Compatibility between XFEL and Ab Initio Structures of the Oxygen Evolving Complex in Photosystem†II.

The Mn4 CaO5 cluster of photosystem II promotes a crucial step in the oxygenic photosynthesis, namely, the water-splitting reaction. The structure of such cluster in the S1 state of the Kok-Joliot's cycle has been recently resolved by femtosecond X-ray free-electron laser (XFEL) measurements. However, the XFEL results are characterized by appreciable discrepancies with previous X-ray diffraction (XRD), as well as with S1 models based on ab initio calculations. We provide here a unifying picture based on a combined set of DFT-based structures and molecular dynamics simulations of the S0 and S1 states. Our findings indicate that the XFEL results cannot be interpreted on the grounds of a single structure. A combination of two S1 stable isomers together with a minority contribution of the S0 state is necessary to reproduce XFEL results within 0.16 Å.

Vibrational fingerprints of the Mn4CaO5 cluster in Photosystem II by mixed quantum-classical molecular dynamics.

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.

Mechanism of Water Delivery to the Active Site of Photosystem II along the S(2) to S(3) Transition.

The two water molecules serving as substrate for the oxygen evolution in Photosystem II are already bound in the S2 state of the Kok-Joliot's cycle. Nevertheless, an additional water molecule is supposed to bind the cluster during the transition between the S2 and S3 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 S2 to S3 transition.

Dynamics of the Special Pair of Chlorophylls of Photosystem II.

Cholophylls are at the basis of the photosynthetic energy conversion mechanisms in algae, plants, and cyanobacteria. In photosystem II, the photoproduced electrons leave a special pair of chlorophylls (namely, P(D1) and P(D2)) that becomes cationic. This oxidizing pair [P(D1),P(D2)](+), in turn, triggers a cascade of oxidative events, eventually leading to water splitting and oxygen evolution. In the present work, using quantum mechanics/molecular mechanics calculations, we investigate the electronic structure and the dynamics of the P(D1)P(D2) special pair in both its oxidized and reduced states. In agreement with previously reported static calculations, the symmetry between the two chlorophylls was found to be broken, the positive charge being preferentially located on P(D1). Nevertheless, this study reveals for the first time that large charge fluctuations occur along dynamics, temporarily inverting the charge preference for the two branches. Finally, a vibrational analysis pinpointed that such charge fluctuations are strongly coupled to specific modes of the special pair.

Reorganization of substrate waters between the closed and open cubane conformers during the S2 to S3 transition in the oxygen evolving complex.

A crucial step in the mechanism for oxygen evolution in the Photosystem II complex resides in the transition from the S2 state to the S3 state of Kok­Joliot's cycle, in which an additional water molecule binds to the cluster. On the basis of computational chemistry calculations on Photosystem II models, we propose a reorganization mechanism involving a hydroxyl (W2) and a µ2-oxo bridge (O5) that is able to link the closed cubane S2B intermediate conformer to the S3 open cubane structure. This mechanism can reconcile the apparent conflict between recently reported water exchange and electron paramagnetic resonance experiments, and theoretical studies.

Characterization of the Sr(2+)- and Cd(2+)-Substituted Oxygen-Evolving Complex of Photosystem II by Quantum Mechanics/Molecular Mechanics Calculations.

The 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 S2 A and closed cubane S2 B 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.

Pathway for Mn-cluster oxidation by tyrosine-Z in the S2 state of photosystem II.

Water 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 S2-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.

Fermi resonance as a tool for probing peridinin environment.

In the present paper, we provide an extended study of the vibrational signature of a butenolide carotenoid, peridinin, in various solvents by combining resonance Raman spectroscopy (RRS) with theoretical calculations. The presence of a Fermi resonance due to coupling between the lactonic C═O stretching and the overtone of the wagging of the C-H in the lactonic ring provides a spectroscopic way of differentiating between peridinins lying in different environments. This is a significant achievement, given that simultaneous presence of several peridinins (each with a peculiar photophysical role) in different environments occurs in the most important peridinin containing proteins, the peridinin-chlorophyll proteins (PCPs) and the Chl a-c2-peridinin binding proteins. In RRS, small modifications of solvent polarity can give rise to large differences in the intensity and splitting between the two bands, resulting from the Fermi resonance. By changing the polarity, we can tune the frequency of stretching of the C═O and, while the C-H wagging frequency is almost always constant in different solvents, move the system from a perfect resonance condition to off-resonance ones. We have corroborated our spectroscopic findings with a quasi-classical dynamical model of two coupled oscillators, and DFT calculations on peridinin in different solvents; we have also used calculations to complete the peridinin vibrational mode assignments in the 800-1600 cm(-1) region of RRS spectra, corresponding to polyene chain motion. Finally, the presence of Fermi resonance has been used to reinterpret previous vibrational spectroscopic experiments in PCPs.

The impact of nitric oxide toxicity on the evolution of the glutathione transferase superfamily: a proposal for an evolutionary driving force.

Glutathione transferases (GSTs) are protection enzymes capable of conjugating glutathione (GSH) to toxic compounds. During evolution an important catalytic cysteine residue involved in GSH activation was replaced by serine or, more recently, by tyrosine. The utility of these replacements represents an enigma because they yield no improvements in the affinity toward GSH or in its reactivity. Here we show that these changes better protect the cell from nitric oxide (NO) insults. In fact the dinitrosyl·diglutathionyl·iron complex (DNDGIC), which is formed spontaneously when NO enters the cell, is highly toxic when free in solution but completely harmless when bound to GSTs. By examining 42 different GSTs we discovered that only the more recently evolved Tyr-based GSTs display enough affinity for DNDGIC (KD < 10(-9) M) to sequester the complex efficiently. Ser-based GSTs and Cys-based GSTs show affinities 10(2)-10(4) times lower, not sufficient for this purpose. The NO sensitivity of bacteria that express only Cys-based GSTs could be related to the low or null affinity of their GSTs for DNDGIC. GSTs with the highest affinity (Tyr-based GSTs) are also over-represented in the perinuclear region of mammalian cells, possibly for nucleus protection. On the basis of these results we propose that GST evolution in higher organisms could be linked to the defense against NO.

Environmental effects on vibrational properties of carotenoids: experiments and calculations on peridinin.

Carotenoids are employed in light-harvesting complexes of dinoflagellates with the two-fold aim to extend the spectral range of the antenna and to protect it from radiation damage. We have studied the effect of the environment on the vibrational properties of the carotenoid peridinin in different solvents by means of vibrational spectroscopies and QM/MM molecular dynamics simulations. Three prototypical solvents were considered: cyclohexane (an apolar/aprotic solvent), deuterated acetonitrile (a polar/aprotic solvent) and methanol (a polar/protic solvent). Thanks to effective normal mode analysis, we were able to assign the experimental Raman and IR bands and to clarify the effect of the solvent on band shifts. In the 1500-1650 cm(-1) region, seven vibrational modes of the polyene chain were identified and assigned to specific molecular vibrations. In the 1700-1800 cm(-1) region a strong progressive down-shift of the lactonic carbonyl frequency is observed passing from cyclohexane to methanol solutions. This has been rationalized here in terms of solvent polarity and solute-solvent hydrogen bond interactions. On the basis of our data we propose a classification of non-equivalent peridinins in the Peridinin-Chlorophyll-Proteins, light-harvesting complexes of dinoflagellates.