Pt nanoparticles under oxidizing conditions - implications of particle size, adsorption sites and oxygen coverage on stability.

Platinum nanoparticles are efficient catalysts for different reactions, such as oxidation of carbon and nitrogen monoxides. Adsorption and interaction of oxygen with the nanoparticle surface, taking place under reaction conditions, determine not only the catalytic efficiency but also the stability of the nanoparticles against oxidation. In this study, platinum nanoparticles in oxygen environment are investigated by systematic screening of initial nanoparticle-oxygen configurations and employing density functional theory and a thermodynamics-based approach. The structures formed at low oxygen coverages are described by adsorption of atomic oxygen on the nanoparticles whereas at high coverages oxide-like species are formed. The relative stability of adsorption configurations at different oxygen coverages, including the phase of fully oxidized nanoparticles, is investigated by constructing p-T phase diagrams for the studied systems.

Structures of Small Platinum Cluster Anions Ptn-: Experiment and Theory.

The structures of platinum cluster anions Pt6--Pt13- have been investigated by trapped ion electron diffraction. Structures were assigned by comparing experimental and simulated scattering functions using candidate structures obtained by density functional theory computations, including spin-orbit coupling. We find a structural evolution from planar structures (Pt6-, Pt7-) and amorphous-like structures (Pt7--Pt9-) to structures based on distorted tetrahedra (Pt9--Pt11-). Finally, Pt12- and Pt13- are based on hcp fragments. While the structural parameters are well described by density functional theory computations for all clusters studied, the predicted lowest energy structure is found in the experiment only for Pt6-. For larger clusters, higher energy isomers are necessary to obtain a fit to the scattering data.

Surprisingly Low Reactivity of Layered Manganese Oxide toward Water Oxidation in Fe/Ni-Free Electrolyte under Alkaline Conditions.

So far, many studies on the oxygen-evolution reaction (OER) by Mn oxides have been focused on activity; however, the identification of the best performing active site and corresponding catalytic cycles is also of critical importance. Herein, the real intrinsic activity of layered Mn oxide toward OER in Fe/Ni-free KOH is studied for the first time. At pH ≈ 14, the onset of OER for layered Mn oxide in the presence of Fe/Ni-free KOH happens at 1.72 V (vs reversible hydrogen electrode (RHE)). In the presence of Fe ions, a 190 mV decrease in the overpotential of OER was recorded for layered Mn oxide as well as a significant decrease (from 172.8 to 49 mV/decade) in the Tafel slope. Furthermore, we find that both Ni and Fe ions increase OER remarkably in the presence of layered Mn oxide, but that pure layered Mn oxide is not an efficient catalyst for OER without Ni and Fe under alkaline conditions. Thus, pure layered Mn oxide and electrolytes are critical factors in finding the real intrinsic activity of layered Mn oxide for OER. Our results call into question the high efficiency of layered Mn oxides toward OER under alkaline conditions and also elucidate the significant role of Ni and Fe impurities in the electrolyte in the presence of layered Mn oxide toward OER under alkaline conditions. Overall, a computational model supports the conclusions from the experimental structural and electrochemical characterizations. In particular, substitutional doping with Fe decreases the thermodynamic OER overpotential up to 310 mV. Besides, the thermodynamic OER onset potential calculated for the Fe-free structures is higher than 1.7 V (vs RHE) and, thus, not in the stability range of Mn oxides.

Oxygen-Evolution Reaction by a Palladium Foil in the Presence of Iron.

Herein, we investigate the oxygen-evolution reaction (OER) and electrochemistry of a Pd foil in the presence of iron under alkaline conditions (pH ≈ 13). As a source of iron, K2FeO4 is employed, which is soluble under alkaline conditions in contrast to many other Fe salts. Immediately after reacting with the Pd foil, [FeO4]2- causes a significant increase in OER and changes in the electrochemistry of Pd. In the absence of this Fe source and under OER, Pd(IV) is stable, and hole accumulation occurs, while in the presence of Fe this accumulation of stored charges can be used for OER. A Density Functional Theory (DFT) based thermodynamic model suggests an oxygen bridge vacancy as an active site on the surface of PdO2 and an OER overpotential of 0.42 V. A substitution of Pd with Fe at this active site reduces the calculated OER overpotential to 0.35 V. The 70 mV decrease in overpotential is in good agreement with the experimentally measured decrease of 60 mV in the onset potential. In the presence of small amounts of Fe salt, our results point toward the Fe doping of PdO2 rather than extra framework FeOx (Fe(OH)3, FeO(OH), and KFeO2) species on top of PdO2 as the active OER sites.

Concentration dependent energy levels shifts in donor-acceptor mixtures due to intermolecular electrostatic interaction.

Recent progress in the improvement of organic solar cells lead to a power conversion efficiency to over 16%. One of the key factors for this improvement is a more favorable energy level alignment between donor and acceptor materials, which demonstrates that the properties of interfaces between donor and acceptor regions are of paramount importance. Recent investigations showed a significant dependence of the energy levels of organic semiconductors upon admixture of different materials, but its origin is presently not well understood. Here, we use multiscale simulation protocols to investigate the molecular origin of the mixing induced energy level shifts and show that electrostatic properties, in particular higher-order multipole moments and polarizability determine the strength of the effect. The findings of this study may guide future material-design efforts in order to improve device performance by systematic modification of molecular properties.

Quantum dynamical simulation of photoinduced electron transfer processes in dye-semiconductor systems: theory and application to coumarin 343 at TiO2.

A recently developed methodology to simulate photoinduced electron transfer processes at dye-semiconductor interfaces is outlined. The methodology employs a first-principles-based model Hamiltonian and accurate quantum dynamics simulations using the multilayer multiconfiguration time-dependent Hartree approach. This method is applied to study electron injection in the dye-semiconductor system coumarin 343-TiO2. Specifically, the influence of electronic-vibrational coupling is analyzed. Extending previous work, we consider the influence of Dushinsky rotation of the normal modes as well as anharmonicities of the potential energy surfaces on the electron transfer dynamics.

Native structure-based modeling and simulation of biomolecular systems per mouse click.

BACKGROUND: Molecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face several challenges: the fastest atomic movements require time steps of a few femtoseconds which are small compared to biomolecular relevant timescales of milliseconds or even seconds for large conformational motions. At the same time, scalability to a large number of cores is limited mostly due to long-range interactions. An appealing alternative to atomic-level simulations is coarse-graining the resolution of the system or reducing the complexity of the Hamiltonian to improve sampling while decreasing computational costs. Native structure-based models, also called Go-type models, are based on energy landscape theory and the principle of minimal frustration. They have been tremendously successful in explaining fundamental questions of, e.g., protein folding, RNA folding or protein function. At the same time, they are computationally sufficiently inexpensive to run complex simulations on smaller computing systems or even commodity hardware. Still, their setup and evaluation is quite complex even though sophisticated software packages support their realization. RESULTS: Here, we establish an efficient infrastructure for native structure-based models to support the community and enable high-throughput simulations on remote computing resources via GridBeans and UNICORE middleware. This infrastructure organizes the setup of such simulations resulting in increased comparability of simulation results. At the same time, complete workflows for advanced simulation protocols can be established and managed on remote resources by a graphical interface which increases reusability of protocols and additionally lowers the entry barrier into such simulations for, e.g., experimental scientists who want to compare their results against simulations. We demonstrate the power of this approach by illustrating it for protein folding simulations for a range of proteins. CONCLUSIONS: We present software enhancing the entire workflow for native structure-based simulations including exception-handling and evaluations. Extending the capability and improving the accessibility of existing simulation packages the software goes beyond the state of the art in the domain of biomolecular simulations. Thus we expect that it will stimulate more individuals from the community to employ more confidently modeling in their research.

Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cß chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

Performance assessment of different constraining potentials in computational structure prediction for disulfide-bridged proteins.

The presence of disulfide bonds in proteins has very important implications on the three-dimensional structure and folding of proteins. An adequate treatment of disulfide bonds in de-novo protein simulations is therefore very important. Here we present a computational study of a set of small disulfide-bridged proteins using an all-atom stochastic search approach and including various constraining potentials to describe the disulfide bonds. The proposed potentials can easily be implemented in any code based on all-atom force fields and employed in simulations to achieve an improved prediction of protein structure. Exploring different potential parameters and comparing the structures to those from unconstrained simulations and to experimental structures by means of a scoring function we demonstrate that the inclusion of constraining potentials improves the quality of final structures significantly. For some proteins (1KVG and 1PG1) the native conformation is visited only in simulations in presence of constraints. Overall, we found that the Morse potential has optimal performance, in particular for the ß-sheet proteins.

Folding path and funnel scenarios for two small disulfide-bridged proteins.

The presence of disulfide bonds leads to an interesting interplay between noncovalent intramolecular interactions and disulfide bond formation even in small proteins. Here we have investigated the folding mechanism of the 23-residue potassium channel blocker 1WQE and the 18-residue antimicrobial peptide protegrin-1 1PG1 , as two proteins containing disulfide bridges, in all-atom basin hopping simulations starting from completely extended conformations. The minimal-energy conformations deviate by only 2.1 and 1.2 A for 1WQE and 1PG1 , respectively, from their structurally conserved experimental conformations. A detailed analysis of their free energy surfaces demonstrates that the folding mechanism of disulfide-bridged proteins can vary dramatically from Levinthal's single-path scenario to a cooperative process consistent with the funnel paradigm of protein folding.

Ground- and excited-state properties of the mixed-valence complex [(NH3)5Ru(III)NCRu(II)(CN)5]-.

A computational study of the ground- and excited-state properties of the mixed-valence complex [(NH 3) 5Ru (III)NCRu (II)(CN) 5] (-) is presented. Employing DFT and TDDFT calculations for the complex in the gas phase and in aqueous solution, we investigate the vibrational and electronic structure of the complex in the electronic ground state as well as the character of the electronically excited states. The relevance of the various excited states for the intervalence metal-metal charge-transfer process in the complex is analyzed based on the change of charge density, spin density, and dipole moment upon photoexcitation as well as by a Mulliken-Hush analysis. Furthermore, those intramolecular modes, which are important for the charge-transfer process, are identified and characterized.

Theoretical study of ultrafast heterogeneous electron transfer reactions at dye-semiconductor interfaces: coumarin 343 at titanium oxide.

A theoretical study of photoinduced heterogeneous electron transfer in the dye-semiconductor system coumarin 343-TiO(2) is presented. The study is based on a generic model for heterogeneous electron transfer reactions, which takes into account the coupling of the electronic states to the nuclear degrees of freedom of coumarin 343 as well as to the surrounding solvent. The quantum dynamics of the electron injection process is simulated employing the recently proposed multilayer formulation of the multiconfiguration time-dependent Hartree method. The results reveal an ultrafast injection dynamics of the electron from the photoexcited donor state into the conduction band of the semiconductor. Furthermore, the mutual influence of electronic injection dynamics and nuclear motion is analyzed in some detail. The analysis shows that--depending on the time scale of nuclear motion--electronic vibrational coupling can result in electron transfer driven by coherent vibrational motion or vibrational motion induced by ultrafast electron transfer.

Stochastic unraveling of time-local quantum master equations beyond the Lindblad class.

A method for stochastic unraveling of general time-local quantum master equations (QME) which involve the reduced density operator at time t only is proposed. The present kind of jump algorithm enables a numerically efficient treatment of QMEs that are not of Lindblad form. So it opens large fields of application for stochastic methods. The unraveling can be achieved by allowing for trajectories with negative weight. We present results for the quantum Brownian motion and the Redfield QMEs as test examples. The algorithm can also unravel non-Markovian QMEs when they are in a time-local form like in the time-convolutionless formalism.