Ab initio tensorial electronic friction for molecules on metal surfaces : nonadiabatic vibrational relaxation

Molecular adsorbates on metal surfaces exchange energy with substrate phonons and low-lying electron-hole pair excitations. In the limit of weak coupling, electron-hole pair excitations can be seen as exerting frictional forces on adsorbates that enhance energy transfer and facilitate vibrational relaxation or hot-electron-mediated chemistry. We have recently reported on the relevance of tensorial properties of electronic friction [M. Askerka et al., Phys. Rev. Lett. 116, 217601 (2016)] in dynamics at surfaces. Here we present the underlying implementation of tensorial electronic friction based on Kohn-Sham density functional theory for condensed phase and cluster systems. Using local atomic-orbital basis sets, we calculate nonadiabatic coupling matrix elements and evaluate the full electronic friction tensor in the Markov limit. Our approach is numerically stable and robust, as shown by a detailed convergence analysis. We furthermore benchmark the accuracy of our approach by calculation of vibrational relaxation rates and lifetimes for a number of diatomic molecules at metal surfaces. We find friction-induced mode-coupling between neighboring CO adsorbates on Cu(100) in a c(2×2) overlayer to be important for understanding experimental findings

NH\u3csub\u3e3\u3c/sub\u3e Binding to the S\u3csub\u3e2\u3c/sub\u3e State of the O\u3csub\u3e2\u3c/sub\u3e-Evolving Complex of Photosystem II: Analogue to H\u3csub\u3e2\u3c/sub\u3eO Binding during the S\u3csub\u3e2\u3c/sub\u3e → S\u3csub\u3e3\u3c/sub\u3e Transition

© 2015 American Chemical Society. 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

Energetics of the S\u3csub\u3e2\u3c/sub\u3e State Spin Isomers of the Oxygen-Evolving Complex of Photosystem II

© 2017 American Chemical Society. 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 S2QA- decay under light-limiting conditions

S\u3csub\u3e3\u3c/sub\u3e State of the O\u3csub\u3e2\u3c/sub\u3e-Evolving Complex of Photosystem II: Insights from QM/MM, EXAFS, and Femtosecond X-ray Diffraction

© 2016 American Chemical Society. 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

Die gegenwaertige Friedensdiskussion in ethischer Perspektive

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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 OEC (oxygen-evolving complex) of PSII are characterized by combined Continuum Electrostatic/Monte Carlo (MCCE), QM/MM and DFT calculations and compared with new and earlier experimental measurements. MCCE shows ammonia has significant affinity at 6 positions but only two significantly influence the OEC. Although the pK$_a$ of ammonium ion is 9.25, it is calculated to only bind as NH$_3$, in agreement with its low affinity at low pH. The calculations also help explain the experimentally observed competitive binding of ammonia with chloride. Ammonia and Cl$^−$ compete for one site. Electrostatic interactions cause Cl$^−$ to effect ammonia at two other sites. Cl$^−$ stabilizes the multiline g = 2.0 form of the S$_2$ state (OEC Mn oxidation state 3444) while ammonia only binds in the g = 4.1 form of the S$_2$ state (oxidation state 4443) due to the movement of the positive charge between Mn1 and Mn4. One ammonia binds near Mn4 and shares a proton with D2-K317, making the ion pair NH$_4$+K317$^0$D61$^-$, making ammonia binding sensitive to the K317A mutation. The affinity of ammonia is also dependent on the protonation state of water 2, a primary ligand to Mn4

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