Theoretical Prediction of S–H Bond Rupture in Methanethiol upon Interaction with Gold

Organic thiols are known to react with gold surface to form self-assembled monolayers (SAMs), which can be used to produce materials with highly attractive properties. Although the structure of various SAMs is widely investigated, some aspects of their formation still represent a matter of debate. One of these aspects is the mechanism of S–H bond dissociation in thiols upon interaction with gold. This work presents a new suggestion for this mechanism on the basis of DFT study of methanethiol interaction with a single gold atom and a Au₂₀ cluster. The reaction path of dissociation is found to be qualitatively independent of the model employed. However, the highest activation barrier of S–H bond dissociation on the single gold atom (12.9 kcal/mol) is considerably lower than that on the Au₂₀ cluster (28.9 kcal/mol), which can be attributed to the higher extent of gold unsaturation. The energy barrier of S–H cleavage decreases by 4.6 kcal/mol in the presence of the second methanethiol molecule at the same adsorption site on the model gold atom. In the case of the Au₂₀ cluster we have observed the phenomenon of hydrogen transfer from one methanethiol molecule to another, which allows reducing the energy barrier of dissociation by 9.1 kcal/mol. This indicates the possibility of the “relay” hydrogen transfer to be the key step of the thiol adsorption observed for the SAMs systems

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

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

NH₃ Binding to the S₂ State of the O₂‑Evolving Complex of Photosystem II: Analogue to H₂O Binding during the S₂ → S₃ Transition

Ammonia binds directly to the oxygen-evolving complex of photosystem II (PSII) upon formation of the S₂ intermediate, as evidenced by electron paramagnetic resonance spectroscopy. We explore the binding mode by using quantum mechanics/molecular mechanics methods and simulations of extended X-ray absorption fine structure spectra. We find that NH₃ binds as an additional terminal ligand to the dangling Mn4, instead of exchanging with terminal water. Because water and ammonia are electronic and structural analogues, these findings suggest that water binds analogously during the S₂ → S₃ transition, leading to rearrangement of ligands in a carrousel around Mn4

X‑ray Free Electron Laser Radiation Damage through the S‑State Cycle of the Oxygen-Evolving Complex of Photosystem II

The oxygen-evolving complex (OEC) catalyzes water-splitting through a reaction mechanism that cycles the OEC through the “S-state” intermediates. Understanding structure/function relationsships of the S-states is crucial for elucidating the water-oxidation mechanism. Serial femtosecond X-ray crystallography has been used to obtain radiation damage-free structures. However, it remains to be established whether “diffraction-before-destruction” is actually accomplished or if significant changes are produced by the high-intensity X-ray pulses during the femtosecond scattering measurement. Here, we use <i>ab initio</i> molecular dynamics simulations to estimate the extent of structural changes induced on the femtosecond time scale. We found that the radiation damage is dependent on the bonding and charge of each atom in the OEC, in a manner that may provide lessons for XFEL studies of other metalloproteins. The maximum displacement of Mn and oxygen centers is 0.25 and 0.39 Å, respectively, during the 50 fs pulse, which is significantly smaller than the uncertainty given the 1.9 Å resolution of the current PSII crystal structures. However, these structural changes might be detectable when comparing isomorphous Fourier differences of electron density maps of the different S-states. One conclusion is that pulses shorter than 15 fs should be used to avoid significant radiation damage

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 <i>S</i> = 1/2 isomer gives rise to a multiline electron paramagnetic resonance (EPR) signal at <i>g</i> = 2.0, whereas the <i>S</i> = 5/2 isomer exhibits a broad EPR signal at <i>g</i> = 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 <i>S</i> = 1/2 state from the <i>S</i> = 5/2 state is exergonic at temperatures above 160 K. However, the <i>S</i> = 1/2 isomer decays to S₁ more slowly than the <i>S</i> = 5/2 isomer. These differences support the hypotheses that the S₃ state is formed via the S₂ state <i>S</i> = 5/2 isomer and that the stabilized S₂ state <i>S</i> = 1/2 isomer plays a role in minimizing S₂Q_A^– decay under light-limiting conditions

Analysis of the Radiation-Damage-Free X‑ray Structure of Photosystem II in Light of EXAFS and QM/MM Data

A recent femtosecond X-ray diffraction study produced the first high-resolution structural model of the oxygen-evolving complex of photosystem II that is free of radiation-induced manganese reduction (Protein Data Bank entries 4UB6 and 4UB8). We find, however, that the model does not match extended X-ray absorption fine structure and QM/MM data for the S₁ state. This is attributed to uncertainty about the positions of oxygen atoms that remain partially unresolved, even at 1.95 Å resolution, next to the heavy manganese centers. In addition, the photosystem II crystals may contain significant amounts of the S₀ state, because of extensive dark adaptation prior to data collection

Ammonia Binding in the Second Coordination Sphere of the Oxygen-Evolving Complex of Photosystem II

Ammonia binds to two sites in the oxygen-evolving complex (OEC) of Photosystem II (PSII). The first is as a terminal ligand to Mn in the S₂ state, and the second is at a site outside the OEC that is competitive with chloride. Binding of ammonia in this latter secondary site results in the S₂ state <i>S</i> = ⁵/₂ spin isomer being favored over the <i>S</i> = ¹/₂ spin isomer. Using electron paramagnetic resonance spectroscopy, we find that ammonia binds to the secondary site in wild-type <i>Synechocystis</i> sp. PCC 6803 PSII, but not in D2-K317A mutated PSII that does not bind chloride. By combining these results with quantum mechanics/molecular mechanics calculations, we propose that ammonia binds in the secondary site in competition with D1-D61 as a hydrogen bond acceptor to the OEC terminal water ligand, W1. Implications for the mechanism of ammonia binding via its primary site directly to Mn4 in the OEC are discussed

S₃ State of the O₂‑Evolving Complex of Photosystem II: Insights from QM/MM, EXAFS, and Femtosecond X‑ray Diffraction

The oxygen-evolving complex (OEC) of photosystem II has been studied in the S₃ state by electron paramagnetic resonance, extended X-ray absorption fine structure (EXAFS), and femtosecond X-ray diffraction (XRD). However, the actual structure of the OEC in the S₃ state has yet to be established. Here, we apply hybrid quantum mechanics/molecular mechanics methods and propose a structural model that is consistent with EXAFS and XRD. The model supports binding of water ligands to the cluster in the S₂ → S₃ transition through a carousel rearrangement around Mn4, inspired by studies of ammonia binding

Fundamental Role of Oxygen Stoichiometry in Controlling the Band Gap and Reactivity of Cupric Oxide Nanosheets

CuO is a nonhazardous, earth-abundant material that has exciting potential for use in solar cells, photocatalysis, and other optoelectronic applications. While progress has been made on the characterization of properties and reactivity of CuO, there remains significant controversy on how to control the precise band gap by tuning conditions of synthetic methods. Here, we combine experimental and theoretical methods to address the origin of the wide distribution of reported band gaps for CuO nanosheets. We establish reaction conditions to control the band gap and reactivity via a high-temperature treatment in an oxygen-rich environment. SEM, TEM, XRD, and BET physisorption reveals little to no change in nanostructure, crystal structure, or surface area. In contrast, UV–vis spectroscopy shows a modulation in the material band gap over a range of 330 meV. A similar trend is found in H₂ temperature-programmed reduction where peak H₂ consumption temperature decreases with treatment. Calculations of the density of states show that increasing the oxygen to copper coverage ratio of the surface accounts for most of the observed changes in the band gap. An oxygen exchange mechanism, supported by ¹⁸O₂ temperature-programmed oxidation, is proposed to be responsible for changes in the CuO nanosheet oxygen to copper stoichiometry. The changes induced by oxygen depletion/deposition serve to explain discrepancies in the band gap of CuO, as reported in the literature, as well as dramatic differences in catalytic performance