Glycerol binding at the narrow channel of photosystem II stabilizes the low-spin S2 state of the oxygen-evolving complex

The oxygen-evolving complex (OEC) of photosystem II (PSII) cycles through redox intermediate states S_i (i = 0-4) during the photochemical oxidation of water. The S₂ state involves an equilibrium of two isomers including the low-spin S₂ (LS-S₂) state with its characteristic electron paramagnetic resonance (EPR) multiline signal centered at g = 2.0, and a high-spin S₂ (HS-S₂) state with its g = 4.1 EPR signal. The relative intensities of the two EPR signals change under experimental conditions that shift the HS-S₂/LS-S₂ state equilibrium. Here, we analyze the effect of glycerol on the relative stability of the LS-S₂ and HS-S₂ states when bound at the narrow channel of PSII, as reported in an X-ray crystal structure of cyanobacterial PSII. Our quantum mechanics/molecular mechanics (QM/MM) hybrid models of cyanobacterial PSII show that the glycerol molecule perturbs the hydrogen-bond network in the narrow channel, increasing the pK_a of D1-Asp61 and stabilizing the LS-S₂ state relative to the HS-S₂ state. The reported results are consistent with the absence of the HS-S₂ state EPR signal in native cyanobacterial PSII EPR spectra and suggest that the narrow water channel hydrogen-bond network regulates the relative stability of OEC catalytic intermediates during water oxidation.

Machine Learning Accelerates Discovery of Optimal Colloidal Quantum Dot Synthesis

Colloidal quantum dots (CQDs) allow broad tuning of the bandgap across the visible and near-infrared spectral regions. Recent advances in applying CQDs in light sensing, photovoltaics, and light emission have heightened interest in achieving further synthetic improvements. In particular, improving monodispersity remains a key priority in order to improve solar cells' open-circuit voltage, decrease lasing thresholds, and improve photodetectors' noise-equivalent power. Here we utilize machine-learning-in-the-loop to learn from available experimental data, propose experimental parameters to try, and, ultimately, point to regions of synthetic parameter space that will enable record-monodispersity PbS quantum dots. The resultant studies reveal that adding a growth-slowing precursor (oleylamine) allows nucleation to prevail over growth, a strategy that enables record-large-bandgap (611 nm exciton) PbS nanoparticles with a well-defined excitonic absorption peak (half-width at half-maximum (hwhm) of 145 meV). At longer wavelengths, we also achieve improved monodispersity, with an hwhm of 55 meV at 950 nm and 24 meV at 1500 nm, compared to the best published to date values of 75 and 26 meV, respectively.

Relative stability of the S2 isomers of the oxygen evolving complex of photosystem II

The oxidation of water to O₂ is catalyzed by the Oxygen Evolving Complex (OEC), a Mn₄CaO₅ complex in Photosystem II (PSII). The OEC is sequentially oxidized from state S₀ to S₄. The S₂ state, (Mn^III)(Mn^IV)₃, coexists in two redox isomers: S_2,g=2, where Mn4 is Mn^IV and S_2,g=4.1, where Mn1 is Mn^IV. Mn4 has two terminal water ligands, whose proton affinity is affected by the Mn oxidation state. The relative energy of the two S₂ redox isomers and the protonation state of the terminal water ligands are analyzed using classical multi-conformer continuum electrostatics (MCCE). The Monte Carlo simulations are done on QM/MM optimized S₁ and S₂ structures docked back into the complete PSII, keeping the protonation state of the protein at equilibrium with the OEC redox and protonation states. Wild-type PSII, chloride-depleted PSII, PSII in the presence of oxidized Y_Z/protonated D1-H190, and the PSII mutants D2-K317A, D1-D61A, and D1-S169A are studied at pH 6. The wild-type PSII at pH 8 is also described. In qualitative agreement with experiment, in wild-type PSII, the S_2,g=2 redox isomer is the lower energy state; while chloride depletion or pH 8 stabilizes the S_2,g=4.1 state and the mutants D2-K317A, D1-D61A, and D1-S169A favor the S_2,g=2 state. The protonation states of D1-E329, D1-E65, D1-H337, D1-D61, and the terminal waters on Mn4 (W1 and W2) are affected by the OEC oxidation state. The terminal W2 on Mn4 is a mixture of water and hydroxyl in the S_2,g=2 state, indicating the two water protonation states have similar energy, while it remains neutral in the S₁ and S_2,g=4.1 states. In wild-type PSII, advancement to S₂ leads to negligible proton loss and so there is an accumulation of positive charge. In the analyzed mutations and Cl^- depleted PSII, additional deprotonation is found upon formation of S₂ state.

Pulsed axial epitaxy of colloidal quantum dots in nanowires enables facet-selective passivation

Epitaxially stacking colloidal quantum dots in nanowires offers a route to selective passivation of defective facets while simultaneously enabling charge transfer to molecular adsorbates - features that must be combined to achieve high-efficiency photocatalysts. This requires dynamical switching of precursors to grow, alternatingly, the quantum dots and nanowires - something not readily implemented in conventional flask-based solution chemistry. Here we report pulsed axial epitaxy, a growth mode that enables the stacking of multiple CdS quantum dots in ZnS nanowires. The approach relies on the energy difference of incorporating these semiconductor atoms into the host catalyst, which determines the nucleation sequence at the catalyst-nanowire interface. This flexible synthetic strategy allows precise modulation of quantum dot size, number, spacing, and crystal phase. The facet-selective passivation of quantum dots in nanowires opens a pathway to photocatalyst engineering: we report photocatalysts that exhibit an order-of-magnitude higher photocatalytic hydrogen evolution rates than do plain CdS quantum dots.

Crystallographic Data Support the Carousel Mechanism of Water Supply to the Oxygen-Evolving Complex of Photosystem II

Photosystem II (PSII) oxidizes water to produce oxygen through a four-step photocatalytic cycle. Understanding PSII structure-function relations is important for the development of biomimetic photocatalytic systems. The quantum mechanics/molecular mechanics (QM/MM) analysis of substrate water binding to the oxygen-evolving complex (OEC) has suggested a rearrangement of water ligands in a carousel mechanism around a key Mn center. Here, we find that the most recently reported X-ray free-electron laser (XFEL) crystallographic data obtained for the dark-stable S₁ state and the doubly flashed S₃ state at 2.25 Å resolution support the carousel mechanism. The features in the XFEL data and QM/MM model-simulated difference Fourier maps suggest that water displacement may occur from the so-called "narrow" channel, resulting in binding of a new water molecule to the OEC, and thus provide new insights into the nature of rearrangements of water ligands along the catalytic cycle before O=O bond formation.

Erratum: Role of Tensorial Electronic Friction in Energy Transfer at Metal Surfaces [Phys. Rev. Lett. 116, 217601 (2016)]

This corrects the article DOI: 10.1103/PhysRevLett.116.217601.

Insights into Photosystem II from Isomorphous Difference Fourier Maps of Femtosecond X-ray Diffraction Data and Quantum Mechanics/Molecular Mechanics Structural Models

Understanding structure-function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods. However, the interpretation of XFEL data from PSII intermediates is challenging because of the issues regarding data-processing, uncertainty on the precise positions of light oxygen atoms next to heavy metal centers, and different kinetics of the S-state transition in microcrystals compared to solution. Here, we summarize recent advances and outstanding challenges in PSII structure-function determination with emphasis on the implementation of quantum mechanics/molecular mechanics techniques combined with isomorphous difference Fourier maps, direct methods, and high-resolution spectroscopy.

Energetics of the S2 State Spin Isomers of the Oxygen-Evolving Complex of Photosystem II

The S₂ redox intermediate of the oxygen-evolving complex in photosystem II is present as two spin isomers. The S = 1/2 isomer gives rise to a multiline electron paramagnetic resonance (EPR) signal at g = 2.0, whereas the S = 5/2 isomer exhibits a broad EPR signal at g = 4.1. The electronic structures of these isomers are known, but their role in the catalytic cycle of water oxidation remains unclear. We show that formation of the S = 1/2 state from the S = 5/2 state is exergonic at temperatures above 160 K. However, the S = 1/2 isomer decays to S₁ more slowly than the S = 5/2 isomer. These differences support the hypotheses that the S₃ state is formed via the S₂ state S = 5/2 isomer and that the stabilized S₂ state S = 1/2 isomer plays a role in minimizing S₂Q_A^- decay under light-limiting conditions.

The O2-Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data

Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn₄O₅ inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage "S" states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves through the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O₂ evolution. The structure of the dark-stable S₁ state has been a target for X-ray crystallography for the past 15 years. However, traditional X-ray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S₁ state. However, the atom positions in this crystal structure are still not consistent with high-resolution EXAFS spectroscopy, partially due to the poorly resolved oxygen positions next to Mn centers and partial reduction due to extended dark adaptation of the sample. These inconsistencies led to the new models of the OEC with an alternative low oxidation state and raised questions on the protonation state of the cluster, especially the O5 μ-oxo bridge. This Account summarizes the most recent models of the OEC that emerged from QM/MM, EXAFS and femtosecond X-ray crystallography methods. When PSII in the S₁ state is exposed to light, the S₁ state is advanced to the higher oxidation states and eventually binds substrate water molecules. Identifying the substrate waters is of paramount importance for establishing the water-oxidation mechanism but is complicated by a large number of spectroscopically similar waters. Water analogues can, therefore, be helpful because they serve as spectroscopic markers that help to track the motion of the substrate waters. Due to a close structural and electronic similarity to water, ammonia has been of particular interest. We review three competing hypotheses on substrate water/ammonia binding and compile theoretical and experimental evidence to support them. Binding of ammonia as a sixth ligand to Mn4 during the S₁ → S₂ transition seems to satisfy most of the criteria, especially the most compelling recent EPR data on D1-D61A mutated PSII. Such a binding mode suggests delivery of water from the "narrow" channel through a "carousel" rearrangement of waters around Mn4 upon the S₂ → S₃ transition. An alternative hypothesis suggests water delivery through the "large" channel on the Ca side. However, both water delivery paths lead to a similar S₃ structure, seemingly reaching consensus on the nature of the last detectable S-state intermediate in the Kok cycle before O₂ evolution.

Characterization of ammonia binding to the second coordination shell of the oxygen-evolving complex of photosystem II

The second-shell ammonia binding sites near the oxygen-evolving complex are characterized by Continuum Electrostatic/Monte Carlo (MCCE), QM/MM and DFT calculations and experimental measurements.

The MOD-QM/MM Method: Applications to Studies of Photosystem II and DNA G-Quadruplexes

Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and catalytic sites embedded in macrobiomolecules (eg, proteins and nucleic acids). QM/MM methodologies are highly efficient since they implement quantum chemistry methods for modeling only the portion of the system involving bond-breaking/forming processes (QM layer), as influenced by the surrounding molecular environment described in terms of molecular mechanics force fields (MM layer). Some of the limitations of QM/MM methods when polarization effects are not explicitly considered include the approximate treatment of electrostatic interactions between QM and MM layers. Here, we review recent advances in the development of computational protocols that allow for rigorous modeling of electrostatic interactions in biomacromolecules and structural refinement, beyond the common limitations of QM/MM hybrid methods. We focus on photosystem II (PSII) with emphasis on the description of the oxygen-evolving complex (OEC) and its high-resolution extended X-ray absorption fine structure spectra (EXAFS) in conjunction with Monte Carlo structural refinement. Furthermore, we review QM/MM structural refinement studies of DNA G4 quadruplexes with embedded monovalent cations and direct comparisons to NMR data.

Role of Tensorial Electronic Friction in Energy Transfer at Metal Surfaces

An accurate description of nonadiabatic energy relaxation is crucial for modeling atomistic dynamics at metal surfaces. Interfacial energy transfer due to electron-hole pair excitations coupled to motion of molecular adsorbates is often simulated by Langevin molecular dynamics with electronic friction. Here, we present calculations of the full electronic friction tensor by using first order time-dependent perturbation theory at the density functional theory level. We show that the friction tensor is generally anisotropic and nondiagonal, as found for hydrogen atom on Pd(100) and CO on Cu(100) surfaces. This implies that electron-hole pair induced nonadiabatic coupling at metal surfaces leads to friction-induced mode coupling, therefore, opening an additional channel for energy redistribution. We demonstrate the robustness and accuracy of our results by direct comparison to established methods and experimental data.

Structural changes in the oxygen-evolving complex of photosystem II induced by the S1 to S2 transition: A combined XRD and QM/MM study

The S₁ → S₂ transition of the oxygen-evolving complex (OEC) of photosystem II does not involve the transfer of a proton to the lumen and occurs at cryogenic temperatures. Therefore, it is commonly thought to involve only Mn oxidation without any significant change in the structure of the OEC. Here, we analyze structural changes upon the S₁ → S₂ transition, as revealed by quantum mechanics/molecular mechanics methods and the isomorphous difference Fourier method applied to serial femtosecond X-ray diffraction data. We find that the main structural change in the OEC is in the position of the dangling Mn and its coordination environment.