1,721,080 research outputs found
Structural and dynamic insights into Mn4Ca cluster-depleted Photosystem II
No full textIn the first steps of natural oxygenic photosynthesis, sunlight is used to oxidize water molecules to protons, electrons and molecular oxygen. This reaction takes place on the Mn4Ca cluster located in the reaction centre of Photosystem II (PSII), where the cluster is assembled and continuously repaired through a process known as photoactivation. Understanding the molecular details of such a process has important implications in different fields, in particular inspiring synthesis and repair strategies for artificial photosynthesis devices. In this regard, a detailed structural and dynamic characterization of Photosystem II lacking a Mn4Ca cluster, namelyapoPSII, is a prerequisite for the full comprehension of the photoactivation. Recently, the structure of theapoPSII was resolved at 2.55 Å resolution [Zhanget al.,eLife, 2017,6, e26933], suggesting a pre-organized structure of the protein cavity hosting the cluster. Anyway, the question of whether these findings are a feature of the method used remains open. Here, by means of classical Molecular Dynamics simulations, we characterized the structural and dynamic features of theapoPSII for different protonation states of the cluster cavity. Albeit an overall conformational stability common to all investigated systems, we found significant deviations in the conformation of the side chains of the active site with respect to the X-ray positions. Our findings suggest that not all residues acting as Mn ligands are pre-organized prior to the Mn4Ca formation and previous local conformational changes are required in order to bind the first Mn ion in the high-affinity binding site
Spin-symmetrised structures and vibrational frequencies of iron-sulfur clusters
No full textCalculations of relaxed geometries of multi-centre transition metal compounds are routinely carried out using Broken Symmetry Density Functional Theory. The resulting low-spin open shell electronic state is described by one single Slater determinant and is affected by spin contamination. To alleviate this symmetry breaking, the Extended Broken Symmetry (EBS) approach can be applied to complexes with an arbitrary number of local high-spin metal ions. The actual symmetry is therefore reconstructed through minimization of an effective Hamiltonian leading to a relaxed geometry consistent with the magnetic couplings. In the present work we extend the approach already introduced by [Chu et al., J. Chem. Theory Comput., 2017, 13, 4675] to the calculation of vibrational frequencies. As prototypes we have considered the iron-sulfur clusters Fe2S2Cl42- and Fe4S4Cl4. We have compared the results obtained for different spin states (high spin, broken symmetry and extended broken symmetry) and by using different DFT functionals (B3LYP, OPBE, BP, M06 and B2PLYP) and a post-HF method (SCS-MP2). The data have shown that for specific vibrational modes the EBS technique produces shifts up to 40 cm-1 with respect to the routinely used Broken Symmetry approach, indicating that the use of a consistent spin-symmetrised state is a crucial ingredient for an accurate description of vibrational properties, as certified by the comparison with the experimental data for the Fe2S2Cl42- cluster. This journal i
Mechanism of Oxygen Evolution and Mn4CaO5 Cluster Restoration in the Natural Water-Oxidizing Catalyst
No full textWater oxidation occurring in the first steps of natural oxygenic photosynthesis is catalyzed by the pigment/protein complex Photosystem II. This process takes place on the Mn4Ca cluster located in the core of Photosystem II and proceeds along the five steps (S0-S4) of the so-called Kok-Joliot cycle until the release of molecular oxygen. The catalytic cycle can therefore be started afresh through insertion of a new water molecule. Here, combining quantum mechanics/molecular mechanics simulations and minimum energy path calculations, we characterized on different spin surfaces the events occurring in the last sector of the catalytic cycle from structural, electronic, and thermodynamic points of view. We found that the process of oxygen evolution and water insertion can be described well by a two-step mechanism, with oxygen release being the rate-limiting step of the process. Moreover, our results allow us to identify the upcoming water molecule required to regenerate the initial structure of the Mn4Ca cluster in the S0 state. The insertion of the water molecule was found to be coupled with the transfer of a proton to a neighboring hydroxide ion, thus resulting in the reconstitution of the most widely accepted model of the S0 state
Optimization strategies in WAHTOR algorithm for quantum computing empirical ansatz: a comparative study
Full text linkBy exploiting the invariance of the molecular Hamiltonian by a unitary transformation of the orbitals it is possible to significantly shorter the depth of the variational circuit in the variational quantum eigensolver (VQE) algorithm by using the wavefunction adapted Hamiltonian through orbital rotation (WAHTOR) algorithm. This work introduces a non-adiabatic version of the WAHTOR algorithm and compares its efficiency with three implementations by estimating quantum processing unit (QPU) resources in prototypical benchmarking systems. Calculating first and second-order derivatives of the Hamiltonian at fixed VQE parameters does not introduce a significant QPU overload, leading to results on small molecules that indicate the non-adiabatic Newton-Raphson method as the more convenient choice. On the contrary, we find out that in the case of Hubbard model systems the trust region non-adiabatic optimization is more efficient. The preset work therefore clearly indicates the best optimization strategies for empirical variational ansatzes, facilitating the optimization of larger variational wavefunctions for quantum computing
Valence-bond states in dynamical Jahn-Teller molecular systems
No full textWe discuss a hopping model of electrons between idealized molecular sites with a local orbital degeneracy and a dynamical Jahn-Teller effect, for crystal field environments of sufficiently high symmetry. For the Mott-insulating case (one electron per site and large Coulomb repulsions), in the simplest twofold degenerate situation, we are led to consider a particular exchange Hamiltonian, describing two isotropic spin-1/2 Heisenberg problems coupled by a quartic term on equivalent bonds. This twin-exchange Hamiltonian applies to a physical regime in which the interorbital singlet is the lowest-energy intermediate state available for hopping. This regime is favored by a relatively strong electron-phonon coupling. Using variational arguments, a largen limit, and exact diagonalization data, we find that the ground state, in the one dimensional case, is a solid valence-bond state. The situation in the two dimensional case is less clear. Finally, the behavior of the system upon hole doping is studied in one dimension
Quantum Monte Carlo study of the Retinal Minimal Model C5H6NH+2
No full text"In this work, we study the electronic and geometrical properties of the ground state of the Retinal Minimal Model C(5) H(6) NH(2) (+) using the variational Monte Carlo (VMC) method by means of the Jastrow antisymmetrized geminal power (JAGP) wavefunction. A full optimization of all wavefunction parameters, including coefficients, and exponents of the atomic basis, has been achieved, giving converged geometries with a compact and correlated wavefunction. The relaxed geometries of the cis and trans isomers present a pronounced bond length alternation pattern characterized by a CC central double bond slightly shorter than that reported by the CASPT2 structures. The comparison between different basis sets indicates converged values of geometrical parameters, energy differences, and dipole moments even when the smallest wavefunction is used. The compactness of the wavefunction as well as the scalability of VMC optimization algorithms on massively parallel computers opens the way to perform full structural optimizations of conjugated biomolecules of hundreds of electrons by correlated methods like Quantum Monte Carlo.
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo
No full textAlthough liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems
STOCHASTIC RESONANCE IN A LASER WITH SATURABLE ABSORBER
No full textWe have investigated, experimentally and theoretically, the occurrence of stochastic resonance (SR) in a laser with saturable absorber: a non-linear optical system presenting optical bistability:and self-pulsed regimes for the laser output intensity. In the optical-bistability regime we have obtained an excellent demonstration of SR by studying Fourier spectra and residence time distributions; operating just below the Hopf bifurcation that originates pulsed periodic regime we have obtained experimental evidence of the SR phenomenon. For operation close to the Hopf bifurcation, the theoretical analysis (performed through numerical simulations) has demonstrated that simultaneous presence of noise and periodic forcing generates excursions far from equilibrium; from the locking between these excursions and periodic forcing the SR phenomenon may arise
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