Leonardo Guidoni

Reaction Pathways for Oxygen Evolution Promoted by Cobalt Catalyst

The in-depth understanding of the molecular mechanisms regulating the water oxidation catalysis is of key relevance for the rationalization and the design of efficient oxygen evolution catalysts based on earth-abundant transition metals. Performing ab initio DFT+U molecular dynamics calculations of cluster models in explicit water solution, we provide insight into the pathways for oxygen evolution of a cobalt-based catalyst (CoCat). The fast motion of protons at the CoCat/water interface and the occurrence of cubane-like Co-oxo units at the catalyst boundaries are the keys to unlock the fast formation of O-O bonds. Along the resulting pathways, we identified the formation of Co(IV)-oxyl species as the driving ingredient for the activation of the catalytic mechanism, followed by their geminal coupling with O atoms coordinated by the same Co. Concurrent nucleophilic attack of water molecules coming directly from the water solution is discouraged by high activation barriers. The achieved results suggest also interesting similarities between the CoCat and the Mn4Ca-oxo oxygen evolving complex of photosystem II.

Water and potassium dynamics inside the KcsA K+ channel

Molecular dynamics simulations and electrostatic modeling are used to investigate structural and dynamical properties of the potassium ions and of water molecules inside the KcsA channel immersed in a membrane‐mimetic environment. Two potassium ions, initially located in the selectivity filter binding sites, maintain their position during 2 ns of dynamics. A third potassium ion is very mobile in the water‐filled cavity. The protein appears engineered so as to polarize water molecules inside the channel cavity. The resulting water induced dipole and the positively charged potassium ion within the cavity are the key ingredients for stabilizing the two K+ ions in the binding sites. These two ions experience single file movements upon removal of the potassium in the cavity, confirming the role of the latter in ion transport through the channel.

The S2 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 S3 State†

One of the key steps in photosynthetic solar-energy conversion performed by plants, algae, and cyanobacteria is the splitting of water into molecular oxygen and hydrogen equivalents.[1] To achieve this challenging task photosynthetic organisms use a protein complex that remained almost unchanged during the evolution in the last two and a half billion years: the photosystem II (PSII). The reaction proceeds by the accumulation of four oxidizing equivalents on the {Mn4CaO5} cluster through five (S0–S4) oxidation states that are sequentially attained during water splitting (Kok cycle).[2] The deep understanding of the way nature has found to perform this difficult task efficiently has a great relevance not only for biology but also for inspiring the development of biomimetic artificial systems that can be used to store solar energy in an environmentally friendly way.[3] Atomic details of the structure of the oxygen-evolving complex (OEC) of PSII have been revealed by extended X-ray absorption fine structure (EXAFS) experiments and by X-ray crystallography at increasing resolution levels.[4] However, the accurate position of the {Mn4CaO5} cluster atoms and its ligands emerged only when a X-ray structure at 1.9 A resolution became accessible.[5] However, the effect of a possible X-ray photo-reduction, in particular on the characterization of the Kok’s state described by this structure and on the unrealistic bond lengths between the oxygen atom O5 and the two manganese ions Mn1 and Mn4, is matter of debate.[6] Additionally, important contributions to the structure refinement came from theoretical studies.[6b,7]

Potassium permeation through the KcsA channel: a density functional study

We present a theoretical study on structural and electronic aspects of K+ permeation through the binding sites of the KcsA channels selectivity filter. Density functional calculations are carried out on models taken from selected snapshots of a molecular dynamics simulation recently reported [FEBS Lett. 477 (2000) 37]. During the translocation process from one binding site to the other, the coordination number of the permeating K+ ion turns out to decrease and K+ ion polarizes significantly its ligands, backbone carbonyl groups and a water molecule. K+-induced polarization increases significantly at the transition state (TS) between the two binding sites. These findings suggest that polarization effects play a significant role in the microscopic mechanisms regulating potassium permeation.

Bathochromic Shift in Green Fluorescent Protein: A Puzzle for QM/MM Approaches

We present an extensive investigation of the vertical excitations of the anionic and neutral forms of wild-type green fluorescent protein using time-dependent density functional theory (TDDFT), multiconfigurational perturbation theory (CASPT2), and quantum Monte Carlo (QMC) methods within a quantum mechanics/molecular mechanics (QM/MM) scheme. The protein models are constructed via room-temperature QM/MM molecular dynamics simulations based on DFT and are representative of an average configuration of the chromophore-protein complex. We thoroughly verify the reliability of our structures through simulations with an extended QM region, different nonpolarizable force fields, as well as partial reoptimization with the CASPT2 approach. When computing the excitations, we find that wave function as well as density functional theory methods with long-range corrected functionals agree in the gas phase with the extrapolation of solution experiments but fail in reproducing the bathochromic shift in the protein, which should be particularly significant in the neutral case. In particular, while all methods correctly predict a shift in the absorption between the anionic and neutral forms of the protein, the location of the theoretical absorption maxima is significantly blue-shifted and too close to the gas-phase values. These results point to either an intrinsic limitation of nonpolarizable force-field embedding in the computation of the excitations or to the need to explore alternative protonation states of amino acids in the close vicinity of the chomophore.

Hybrid QM/MM Car-Parrinello simulations of catalytic and enzymatic reactions

A review. First-principles mol. dynamics (Car-Parrinello) simulations based on d. functional theory have emerged as a powerful tool for the study of phys., chem. and biol. systems. At present, using parallel computers, systems of a few hundreds of atoms can be routinely investigated. By extending this method to a mixed quantum mech. - mol. mech. (QM/MM) hybrid scheme, the system size can be enlarged further. Such an approach is esp. attractive for the in situ investigation of chem. reactions that occur in a complex and heterogeneous environment. Here, we review some recent applications of hybrid Car-Parrinello simulations of chem. and biol. systems as illustrative examples of the current potential and limitations of this promising novel technique. [on SciFinder (R)]

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

Significance A key step in natural photosynthesis is the water-splitting reaction into molecular oxygen and hydrogen equivalents. Understanding the molecular mechanisms behind this photoreaction will unravel the secrets of solar energy conversion in biochemistry and may inspire the design of artificial biomimetic materials for green energy production. Photosynthetic water oxidation occurs in the Mn4Ca core of the photosystem II complex and proceeds through five subsequent steps S0 – S4 of the Kok cycle. Four electrons are sequentially removed from the Mn4Ca core by a nearby tyrosine, which is in turn oxidized by the photoactivated chlorophyll special pair. Using first principles multiscale atomistic simulations we clarify the thermodynamics and the kinetics for such electron abstraction in the S2 state. 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, S2A and S2B 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 S2B 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 S2B conformation, providing the basis for a structural model of the S3 state.

Ab Initio Geometry and Bright Excitation of Carotenoids: Quantum Monte Carlo and Many Body Green’s Function Theory Calculations on Peridinin

In this letter, we report the singlet ground state structure of the full carotenoid peridinin by means of variational Monte Carlo (VMC) calculations. The VMC relaxed geometry has an average bond length alternation of 0.1165(10) Å, larger than the values obtained by DFT (PBE, B3LYP, and CAM-B3LYP) and shorter than that calculated at the Hartree-Fock (HF) level. TDDFT and EOM-CCSD calculations on a reduced peridinin model confirm the HOMO-LUMO major contribution of the Bu(+)-like (S2) bright excited state. Many Body Greens Function Theory (MBGFT) calculations of the vertical excitation energy of the Bu(+)-like state for the VMC structure (VMC/MBGFT) provide an excitation energy of 2.62 eV, in agreement with experimental results in n-hexane (2.72 eV). The dependence of the excitation energy on the bond length alternation in the MBGFT and TDDFT calculations with different functionals is discussed.

Coordination Numbers of K+ and Na+ Ions Inside the Selectivity Filter of the KcsA Potassium Channel: Insights from First Principles Molecular Dynamics

Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of K(+) and Na(+) ions in the selectivity filter of the KcsA channel, and in water. At the DFT/BLYP level, K(+) ions were found to display an average coordination number of 6.6 in the filter, and 6.2 in water. Na(+) ions displayed an average coordination number of 5.2 in the filter, and 5.0 in water. A comparison was made with the average coordination numbers obtained from using classical molecular dynamics (6.7 for K(+) in the filter, 6.6 for K(+) in water, 6.0 for Na(+) in the filter, and 5.2 for Na(+) in water). The observation that different coordination numbers were displayed by the ions in QM/MM simulations and in classical molecular dynamics is relevant to the discussion of selectivity in K-channels.

Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo

Although 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.