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X-ray absorption spectroscopy yields direct access to the electronic and geometric structure of hybrid inorganic-organic interfaces formed upon adsorption of complex molecules at metal surfaces. The unambiguous interpretation of corresponding spectra is challenged by the intrinsic geometric flexibility of the adsorbates and the chemical interactions with the interface. Density-functional theory (DFT) calculations of the extended adsorbate-substrate system are an established tool to guide peak assignment in X-ray photoelectron spectroscopy (XPS) of complex interfaces. We extend this to the simulation and interpretation of X-ray absorption spectroscopy (XAS) data in the context of functional organic molecules on metal surfaces using dispersion-corrected DFT calculations within the transition potential approach. On the example of X-ray absorption signatures for the prototypical case of 2H-porphine adsorbed on Ag(111) and Cu(111) substrates, we follow the two main effects of the molecule/surface interaction on XAS: (1) the substrate-induced chemical shift of the 1s core levels that dominates in physisorbed systems and (2) the hybridization-induced broadening and loss of distinct resonances that dominates in more chemisorbed systems., 13 pages, 4 figures

Lithium-titanium-oxide (Li

We present a perturbation approach rooted in time-dependent density-functional theory to calculate electron hole (eh)-pair excitation spectra during the non-adiabatic vibrational damping of adsorbates on metal surfaces. Our analysis for the benchmark systems CO on Cu(100) and Pt(111) elucidates the surprisingly strong influence of rather short electronic coherence times. We demonstrate how in the limit of short electronic coherence times, as implicitly assumed in prevalent quantum nuclear theories for the vibrational lifetimes as well as electronic friction, band structure effects are washed out. Our results suggest that more accurate lifetime or chemicurrent-like experimental measurements could characterize the electronic coherence., Comment: Article as accepted for publication in Physical Review Letters

Implicit solvation calculations based on a Stern-layer corrected size-modified Poisson-Boltzmann (SMPB) model are an effective approach to capture electrolytic effects in first-principles electronic structure calculations. For a given salt solution, they require a range of ion-specific parameters, which describe the size of the dissolved ions as well as thickness and shape of the Stern layer. Out of this defined parameter space, we show that the Stern layer thickness expressed in terms of the solute’s electron density and the resulting ionic cavity volume completely determine ion effects on the stability of neutral solutes. Using the efficient SMPB functionality of the full-potential density-functional theory package FHI-aims, we derive optimized such Stern layer parameters for neutral solutes in various aqueous monovalent electrolytes. The parametrization protocol relies on fitting to reference Setschenow coefficients that describe solvation free energy changes with ionic strength at low to medium concentrations. The availability of such data for NaCl solutions yields a highly predictive SMPB model that allows to recover the measured Setschenow coefficients with an accuracy that is comparable to prevalent quantitative regression models. Correspondingly derived SMPB parameters for other salts suffer from a much scarcer experimental data base but lead to Stern layer properties that follow a physically reasonable trend with ionic hydration numbers.

The CHARMM, general Amber and OPLS force fields are evaluated for their suitability in simulating the molecular dynamics of the dissolution of the hydrophobic, small-molecule active pharmaceutical ingredients aspirin, ibuprofen, and paracetamol in aqueous media. The force fields are evaluated by comparison with quantum chemical simulations or experimental references on the basis of the following capabilities: accurately representing intra- and intermolecular interactions, appropriately reproducing crystal lattice parameters, adequately describing thermodynamic properties, and the qualitative description of the dissolution behavior. To make this approach easily accessible for evaluating the dissolution properties of novel drug candidates in the early stage of drug development, the force field parameter files are generated using online resources such as the SWISS PARAM servers, and the software packages ACPYPE and Maestro. All force fields are found to reproduce the intermolecular interactions with a reasonable degree of accuracy, with the general Amber and CHARMM force fields showing the best agreement with quantum mechanical calculations. A stable crystal bulk structure is obtained for all model substances, except for ibuprofen, where the reproductions of the lattice parameters and observed crystal stability are considerably poor for all force fields. The heat of solution used to evaluate the solid-to-solution phase transitions is found to be in qualitative agreement with the experimental data for all combinations tested, with the results being quantitatively optimum for the general Amber and CHARMM force fields. For aspirin and paracetamol, stable crystal–water interfaces were obtained. The (100), (110), (011) and (001) interfaces of aspirin or paracetamol and water were simulated for each force field for 30 ns. Although generally expected as a rare event, in some of the simulations, dissolution is observed at 310 K and ambient pressure conditions.

We present a molecular simulation approach to efficiently determine quantitative rate constants for rare dissolution events from organic crystals. Metadynamics is employed to generate a tailored bias potential that accelerates the escape from the bound state in subsequent hyperdynamics simulations. The robustness and acceleration obtained in the application to kink site dissolution at the aspirin(001)/water interface suggests this technique as a suitable tool to unravel the atomic-scale mechanisms of crystal dissolution.

Kinetic Monte Carlo (kMC) simulations have emerged as a key tool for microkinetic modeling in heterogeneous catalysis and other materials applications. Systems, where site-specificity of all elementary reactions allows a mapping onto a lattice of discrete active sites, can be addressed within the particularly efficient lattice kMC approach. To this end we describe the versatile kmos software package, which offers a most user-friendly implementation, execution, and evaluation of lattice kMC models of arbitrary complexity in one- to three-dimensional lattice systems, involving multiple active sites in periodic or aperiodic arrangements, as well as site-resolved pairwise and higher-order lateral interactions. Conceptually, kmos achieves a maximum runtime performance which is essentially independent of lattice size by generating code for the efficiency-determining local update of available events that is optimized for a defined kMC model. For this model definition and the control of all runtime and evaluation aspects kmos offers a high-level application programming interface. Usage proceeds interactively, via scripts, or a graphical user interface, which visualizes the model geometry, the lattice occupations and rates of selected elementary reactions, while allowing on-the-fly changes of simulation parameters. We demonstrate the performance and scaling of kmos with the application to kMC models for surface catalytic processes, where for given operation conditions (temperature and partial pressures of all reactants) central simulation outcomes are catalytic activity and selectivities, surface composition, and mechanistic insight into the occurrence of individual elementary processes in the reaction network., Comment: 21 pages, 12 figures

Wir prasentieren eine Einbettungstechnik fur metallische Systeme, die es ermoglicht, Energiedissipation in Substratphononen wahrend chemischer Reaktionen ausgehend von ersten Prinzipien zu modellieren. Die Trennung von chemischen und elastischen Beitragen zum Wechselwirkungspotential liefert eine quantitative Beschreibung von elektronischer und phononischer Bandstruktur. Eine Anwendung auf O2-Dissoziation auf Pd(100) sagt in ihren Translationsfreiheitsgraden “heise” Sauerstoffadatome als eine Folge der dabei freigesetzten Energie (rund 2.6 eV) voraus. Dies stellt die instantane Thermalisierung von Reaktionsenthalpien in Frage, die sonst in der Modellierung von heterogener Katalyse angenommen wird.

(Semi)local density functional approximations (DFAs) are the workhorse electronic structure methods in condensed matter theory and surface science. The correlation energy density ϵc(r) (a spatial function that yields the correlation energy Ec upon integration) is central to defining such DFAs. Unlike Ec, ϵc(r) is not uniquely defined, however. Indeed, there are infinitely many functions that integrate to the correct Ec for a given electron density ρ. The challenge for constructing useful DFAs is thus to find a suitable connection between ϵc(r) and ρ. Herein, we present a new such approach by deriving ϵc(r) directly from the coupled-cluster (CC) energy expression. The corresponding energy densities are analyzed for prototypical two-electron systems. As a proof-of-principle, we construct a semilocal functional to approximate the numerical CC correlation energy densities. Importantly, the energy densities are not simply used as reference data but guide the choice of the functional form, leading to a remarkably simple and accurate correlation functional for the helium isoelectronic series. While the resulting functional is not transferable to many-electron systems (due to a lack of same-spin correlation), these results underscore the potential of the presented approach.

The fabrication of highly active and robust hexagonal ruthenium oxide nanosheets for the electrocatalytic oxygen evolution reaction (OER) in an acidic environment is reported. The ruthenate nanosheets exhibit the best OER activity of all solution-processed acid medium electrocatalysts reported to date, reaching 10 mA cm(-2) at an overpotential of only approximate to 255 mV. The nanosheets also demonstrate robustness under harsh oxidizing conditions. Theoretical calculations give insights into the OER mechanism and reveal that the edges are the origin of the high OER activity of the nanosheets. Moreover, the post OER analyses indicate, apart from coarsening, no observable change in the morphology of the nanosheets or oxidation states of ruthenium during the electrocatalytic process. Therefore, the present investigation suggests that ruthenate nanosheets are a promising acid medium OER catalyst with application potential in proton exchange membrane electrolyzers and beyond.

Carbon Capture and Sequestration (CCS) is one of the promising ways to significantly reduce the CO2 emission from power plants. In particular, amongst several separation strategies, adsorption by nano-porous materials is regarded as a potential means to efficiently capture CO2 at the place of its origin in a post-combustion process. The search for promising materials in such a process not only requires the screening of a multitude of materials but also the development of an adequate evaluation metric. Several evaluation criteria have been introduced in the literature concentrating on a single adsorption or material property at a time. Parasitic energy is a new approach for material evaluation to address the energy load imposed on a power plant while applying CCS. In this work, we evaluate over 60 different materials with respect to their parasitic energy, including experimentally realized and hypothetical materials such as metal–organic frameworks (MOFs), zeolitic imidazolate frameworks (ZIFs), porous polymer networks (PPNs), and zeolites. The results are compared to other proposed evaluation criteria and performance differences are studied regarding the regeneration modes, (i.e. Pressure-Swing (PSA) and Temperature-Swing Adsorption (TSA)) as well as the flue gas composition.

We present first-principles kinetic Monte Carlo (1p-kMC) simulations addressing the CO oxidation reaction at Pd(100) for gas-phase conditions ranging from ultra-high vacuum to ambient pressures and elevated temperatures. For the latter technologically relevant regime there is a long-standing debate regarding the nature of the active surface. The pristine metallic surface, an ultra-thin $$(\sqrt{5}\times \sqrt{5})R27^{\circ}$$ PdO(101) surface oxide, and thicker oxide layers have each been suggested as the active state. We investigate these hypotheses with 1p-kMC simulations focusing on either the Pd(100) surface or the PdO(101) surface oxide and intriguingly obtain a range of (T, p)-conditions where both terminations appear metastable. The predicted bistability regime nicely ties in with oscillatory behavior reported experimentally by Hendriksen et al. (Catal Today 105:234, 2005). Within this regime we find that both surface terminations exhibit very similar intrinsic reactivity, which puts doubts on attempts to assign the catalytic function to just one active state.

An asymmetric turn: Scanning tunneling spectroscopy has been used to analyze the structure of tris[4-(phenylazo)phenyl)]amine on a Au(111) surface. A degenerate marker state serves as a sensitive probe for the structure of the adsorbed molecules.

Density-functional theory based global geometry optimization is employed to systematically scrutinize the possibility of multidoping of hydrogenated Si clusters to achieve high spin states beyond the septet limit of a single-atom dopant. While our unbiased configurational search reveals that the previously suggested Si18H12 double hexagonal prism structure is generally too small to accommodate two dopants in magnetized state, the larger Si24H24 cage turns out to be suitable for such applications. For dimer dopants M2+ = Cr2+, Mn2+, and CrMn+, the structural integrity of the host cage is conserved in the ground-state structure of corresponding M2+@Si24H24 aggregates, as is the unusually high spin state of the guest dopant, which in the case of Cr2+ already exceeds the single-atom dopant septet limit by almost a factor of 2. Moreover, the possibility of further increasing the cluster spin moment by encapsulating an even larger number of dopants into a suitably sized hydrogenated Si cage is illustrated for the example of a (CrMn+)2@Si28H28 aggregate with a total number of 18 unpaired electrons. These results strongly suggest multidoping of Si clusters as a viable route to novel cluster-based materials for magneto-optic applications.

We present a DFT-based Wulff construction of the equilibrium shape of RuO2 particles in an oxygen environment. The obtained intricate variations in the crystal habit with the oxygen chemical potential allow for a detailed discussion of the dependence on the oxidising pretreatment used in recent powder catalyst studies. The analysis specifically indicates an incomplete particle shape equilibration in previously used low-temperature calcination. Equilibrated particles could be active CO oxidation catalysts with long-term stability in oxidising feed and then represent an interesting alternative to the previously suggested core–shell concept.

First-principles screening approaches exploiting energy trends in surface adsorption represent an unparalleled success story in recent computational catalysis research. Here we argue that our still limited understanding of the structure of active sites is one of the major bottlenecks towards an ever extended and reliable use of such computational screening for catalyst discovery. For low-index transition metal surfaces, the prevalently chosen high-symmetry (terrace and step) sites offered by the nominal bulk-truncated crystal lattice might be justified. For more complex surfaces and composite catalyst materials, computational screening studies will need to actively embrace a considerable uncertainty with respect to what truly are the active sites. By systematically exploring the space of possible active site motifs, such studies might eventually contribute towards a targeted design of optimized sites in future catalysts.

In the future, (electro‐)chemical catalysts will have to be more tolerant towards a varying supply of energy and raw materials. This is mainly due to the fluctuating nature of renewable energies. For example, power‐to‐chemical processes require a shift from steady‐state operation towards operation under dynamic reaction conditions. This brings along a number of demands for the design of both catalysts and reactors, because it is well‐known that the structure of catalysts is very dynamic. However, in‐depth studies of catalysts and catalytic reactors under such transient conditions have only started recently. This requires studies and advances in the fields of 1) operando spectroscopy including time‐resolved methods, 2) theory with predictive quality, 3) kinetic modelling, 4) design of catalysts by appropriate preparation concepts, and 5) novel/modular reactor designs. An intensive exchange between these scientific disciplines will enable a substantial gain of fundamental knowledge which is urgently required. This concept article highlights recent developments, challenges, and future directions for understanding catalysts under dynamic reaction conditions.

We augment ab initio molecular dynamics simulations with a quantitative account of phononic dissipation to study the non-equilibrium aftermath of the exothermic oxygen dissociation at low-index (111), (100), and (110) Pd surfaces. Comparing the hyperthermal diffusion arising from a non-instantaneous dissipation of the released chemical energy, we find a striking difference in the resulting "hot" adatom lifetime that is not overall reflected in experimentally recorded product end distances. We rationalize this finding through a detailed mode-specific phonon analysis and identify the dominant dissipation channels as qualitatively different groups of localized surface modes that ultimately lead to intrinsically different rates of dissipation to the Pd bulk. The thus obtained first-principles perspective on non-equilibrium adsorbate-phonon dynamics thereby underscores the sensitive dependence on details of the phononic fine structure, while questioning prevalent assumptions about energy sinks made in commonly used model bath Hamiltonians.

We augment ab initio molecular dynamics simulations with a quantitative account of phononic dissipation to study the non-equilibrium aftermath of the exothermic oxygen dissociation at low-index (111), (100), and (110) Pd surfaces. Comparing the hyperthermal diffusion arising from a non-instantaneous dissipation of the released chemical energy, we find a striking difference in the resulting "hot" adatom lifetime that is not overall reflected in experimentally recorded product end distances. We rationalize this finding through a detailed mode-specific phonon analysis and identify the dominant dissipation channels as qualitatively different groups of localized surface modes that ultimately lead to intrinsically different rates of dissipation to the Pd bulk. The thus obtained first-principles perspective on non-equilibrium adsorbate-phonon dynamics thereby underscores the sensitive dependence on details of the phononic fine structure, while questioning prevalent assumptions about energy sinks made in commonly used model bath Hamiltonians.

Blue-color stimulated emission with low threshold power is observed from In- and Zn-MOFs, which feature a highly fluorescent chromophore densely packed and rigidly linked to the metal-ion centers in the solid state. The density-of-states and transition dipole moments are calculated and the stimulated emission phenomenon is correlated with these properties. MOE (Min. of Education, S’pore) Accepted version

Realistic oxide materials are often semiconductors, in particular at elevated temperatures, and their surfaces contain undercoordiated atoms at structural defects such as steps and corners. Using hybrid density-functional theory and ab initio atomistic thermodynamics, we investigate the interplay of bond-making, bond-breaking, and charge-carrier trapping at the corner defects at the (100) surface of a p-doped MgO in thermodynamic equilibrium with an O2 atmosphere. We show that by manipulating the coordination of surface atoms one can drastically change and even reverse the order of stability of reduced versus oxidized surface sites., Comment: 5 papges, 4 figures

Multi‐photon absorption (MPA) is among the most prominent nonlinear optical (NLO) effects and has applications, for example in telecommunications, defense, photonics, and bio‐medicines. Established MPA materials include dyes, quantum dots, organometallics and conjugated polymers, most often dispersed in solution. We demonstrate how metal–organic frameworks (MOFs), a novel NLO solid‐state materials class, can be designed for exceptionally strong MPA behavior. MOFs consisting of zirconium‐ and hafnium‐oxo‐clusters and featuring a chromophore linker based on the tetraphenylethene (TPE) molecule exhibit record high two‐photon absorption (2PA) cross‐section values, up to 3600 GM. The unique modular building‐block principle of MOFs allows enhancing and optimizing their MPA properties in a theory‐guided approach by combining tailored charge polarization, conformational strain, three‐dimensional arrangement, and alignment of the chromophore linkers in the crystal. MOE (Min. of Education, S’pore) Accepted version

We explicitly calculate the free-energy barrier for the initial proton abstraction in the water splitting reaction at rutile ${\mathrm{TiO}}_{2}(110)$ through ab initio molecular dynamics. Combining solid-state embedding, an energy based reaction coordinate and state-of-the-art free-energy reconstruction techniques renders the calculation tractable at the hybrid density-functional theory level. The obtained free-energy barrier of approximately 0.2 eV, depending slightly on the orientation of the first acceptor water molecule, suggests a hindered reaction on the pristine rutile surface.

Coupled-cluster theory with single, double, and perturbative triple excitations (CCSD(T)) is widely considered to be the "gold standard" of ab initio quantum chemistry. Using the domain-based pair natural orbital local correlation concept (DLPNO-CCSD(T)), these calculations can be performed on systems with hundreds of atoms at an accuracy of ∼99.9% of the canonical CCSD(T) method. This allows for ab initio calculations providing reference adsorption energetics at solid surfaces with an accuracy approaching 1 kcal/mol. This is an invaluable asset, not least for the assessment of density functional theory (DFT) as the prevalent approach for large-scale production calculations in energy or catalysis applications. Here we use DLPNO-CCSD(T) with embedded cluster models to compute entire adsorbate potential energy surfaces for the binding of a set of prototypical closed-shell molecules (H

The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices´ for performing CSP calculations. All of the targets, apart from a single potentially disordered Z?? = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms. Fil: Reilly, Anthony M.. Cambridge Crystallographic Data Centre; Fil: Cooper, Richard I.. Chemistry Research Laboratory; Fil: Adjiman, Claire S.. Imperial College London; Reino Unido Fil: Bhattacharya, Saswata. Fritz Haber Institute Of The Max Planck Society; Fil: Boese, A. Daniel. Karl-franzens-universitat Graz; Austria Fil: Brandenburg, Jan Gerit. Colegio Universitario de Londres; Reino Unido. Universitat Bonn; Alemania Fil: Bygrave, Peter J.. University of Southampton; Reino Unido Fil: Bylsma, Rita. Radboud Universiteit Nijmegen; Países Bajos Fil: Campbell, Josh E.. University of Southampton; Reino Unido Fil: Car, Roberto. University of Princeton; Estados Unidos Fil: Case, David H.. University of Southampton; Reino Unido Fil: Chadha, Renu. University Institute Of Pharmaceutical Sciences India; India Fil: Cole, Jason C.. Cambridge Crystallographic Data Centre; Fil: Cosburn, Katherine. University of Tulane; Estados Unidos. University of Toronto; Canadá Fil: Cuppen, Herma M.. Radboud Universiteit Nijmegen; Países Bajos Fil: Curtis, Farren. University of Tulane; Estados Unidos. University of Carnegie Mellon; Estados Unidos Fil: Day, Graeme M.. University of Southampton; Reino Unido Fil: DiStasio, Robert A.. University of Princeton; Estados Unidos. Cornell University; Estados Unidos Fil: Dzyabchenko, Alexander. Karpov Institute Of Physical Chemistry; Fil: Van Eijck, Bouke P.. University of Utrecht; Países Bajos. Utrecht University; Países Bajos Fil: Elking, Dennis M.. Openeye Scientific Software, Inc; Fil: Van Den Ende, Joost A.. Radboud Universiteit Nijmegen; Países Bajos Fil: Facelli, Julio C.. University of Utah; Estados Unidos Fil: Ferraro, Marta B.. Universidad de Buenos Aires; Argentina Fil: Fusti-Molnar, Laszlo. Openeye Scientific Software, Inc; Fil: Gatsiou, Christina-Anna. Imperial College London; Reino Unido Fil: Gee, Thomas S.. University of Southampton; Reino Unido Fil: De Gelder, René. Radboud Universiteit Nijmegen; Países Bajos Fil: Ghiringhelli, Luca M.. Fritz Haber Institute Of The Max Planck Society; Fil: Goto, Hitoshi. Toyohashi University Of Technology; Fil: Grimme, Stefan. Universitat Bonn; Alemania Fil: Guo, Rui. Colegio Universitario de Londres; Reino Unido Fil: Hofmann, Detlef W. M.. Flexcryst; . Polaris; Fil: Hoja, Johannes. Fritz Haber Institute Of The Max Planck Society; Fil: Hylton, Rebecca K.. Colegio Universitario de Londres; Reino Unido Fil: Iuzzolino, Luca. Colegio Universitario de Londres; Reino Unido Fil: Jankiewicz, Wojciech. University Of Silesia In Katowice; Fil: De Jong, Daniël T.. Radboud Universiteit Nijmegen; Países Bajos Fil: Kendrick, John. University Of Bradford; Fil: De Klerk, Niek J. J.. Radboud Universiteit Nijmegen; Países Bajos Fil: Ko, Hsin-Yu. University of Princeton; Estados Unidos Fil: Kuleshova, Liudmila N.. Flexcryst; Fil: Li, Xiayue. University of Tulane; Estados Unidos. Argonne National Laboratory; Estados Unidos Fil: Lohani, Sanjaya. University of Tulane; Estados Unidos Fil: Leusen, Frank J. J.. University Of Bradford; Fil: Lund, Albert M.. University of Utah; Estados Unidos. Openeye Scientific Software, Inc; Fil: Lv, Jian. Jilin University; China Fil: Ma, Yanming. Jilin University; China Fil: Marom, Noa. University of Carnegie Mellon; Estados Unidos. University of Tulane; Estados Unidos Fil: Masunov, Artëm E.. University Of Central Florida; . National Research Nuclear University Mephi; Fil: McCabe, Patrick. Cambridge Crystallographic Data Centre; Fil: McMahon, David P.. University of Southampton; Reino Unido Fil: Meekes, Hugo. Radboud Universiteit Nijmegen; Países Bajos Fil: Metz, Michael P.. University Of Delaware; Fil: Misquitta, Alston J.. Queen Mary, University Of London; Fil: Mohamed, Sharmarke. Khalifa University Of Science And Technology; Fil: Monserrat, Bartomeu. Rutgers, The State University Of New Jersey; . University of Cambridge; Estados Unidos Fil: Needs, Richard J.. University of Cambridge; Estados Unidos Fil: Neumann, Marcus A.. No especifica; Fil: Nyman, Jonas. University of Southampton; Reino Unido Fil: Obata, Shigeaki. Toyohashi University Of Technology; Fil: Oberhofer, Harald. Universitat Technical Zu Munich; Alemania Fil: Oganov, Artem R.. Northwestern Polytechnical University; China. Skolkovo Institute Of Science And Technology; . Moscow Institute Of Physics And Technology; . Stony Brook University; Fil: Orendt, Anita M.. University of Utah; Estados Unidos Fil: Pagola, Gabriel Ignacio. Universidad de Buenos Aires; Argentina Fil: Pantelides, Constantinos C.. Imperial College London; Reino Unido Fil: Pickard, Chris J.. University of Cambridge; Estados Unidos. Colegio Universitario de Londres; Reino Unido Fil: Podeszwa, Rafal. University Of Silesia In Katowice; Fil: Price, Louise S.. Colegio Universitario de Londres; Reino Unido Fil: Price, Sarah L.. Colegio Universitario de Londres; Reino Unido Fil: Pulido, Angeles. University of Southampton; Reino Unido Fil: Read, Murray G.. Cambridge Crystallographic Data Centre; Fil: Reuter, Karsten. Universitat Technical Zu Munich; Alemania Fil: Schneider, Elia. University of New York; Estados Unidos Fil: Schober, Christoph. Universitat Technical Zu Munich; Alemania Fil: Shields, Gregory P.. Cambridge Crystallographic Data Centre; Fil: Singh, Pawanpreet. University Institute Of Pharmaceutical Sciences India; India Fil: Sugden, Isaac J.. Imperial College London; Reino Unido Fil: Szalewicz, Krzysztof. University Of Delaware; Fil: Taylor, Christopher R.. University of Southampton; Reino Unido Fil: Tkatchenko, Alexandre. University Of Luxembourg; . Fritz Haber Institute Of The Max Planck Society; Fil: Tuckerman, Mark E.. University of New York; Estados Unidos. New York University Shanghai; China. Courant Institute Of Mathematical Sciences; Fil: Vacarro, Francesca. University of Tulane; Estados Unidos. Loyola University New Orleans; Fil: Vasileiadis, Manolis. Imperial College London; Reino Unido Fil: Vazquez-Mayagoitia, Alvaro. Argonne National Laboratory; Estados Unidos Fil: Vogt, Leslie. University of New York; Estados Unidos Fil: Wang, Yanchao. Jilin University; China Fil: Watson, Rona E.. Colegio Universitario de Londres; Reino Unido Fil: De Wijs, Gilles A.. Radboud Universiteit Nijmegen; Países Bajos Fil: Yang, Jack. University of Southampton; Reino Unido Fil: Zhu, Qiang. Stony Brook University; Fil: Groom, Colin R.. Cambridge Crystallographic Data Centre

Low carrier mobilities still hamper the use of organic semiconductors in many applications. Using a staged virtual screening approach we compute the electronic couplings and intramolecular reorganization energies as two main descriptors for charge mobility for a set of 95 445 molecular crystals extracted from the Cambridge Structural Database (CSD). As a final step, on the basis of the calculated coupling values, we identify materials with long-range charge percolation pathways. Thus we readily find many acclaimed compounds as well as a number of most promising materials that have not yet been considered for an application in organic electronics. Together with the unique metadata provided in the CSD, the large descriptor database allows us to extract important trends and correlations that will further accelerate the theoretical design and discovery of high mobility organic semiconductors.

We explicitly calculate the free-energy barrier for the initial proton abstraction in the water splitting reaction at rutile TiO_{2}(110) through ab initio molecular dynamics. Combining solid-state embedding, an energy based reaction coordinate and state-of-the-art free-energy reconstruction techniques renders the calculation tractable at the hybrid density-functional theory level. The obtained free-energy barrier of approximately 0.2 eV, depending slightly on the orientation of the first acceptor water molecule, suggests a hindered reaction on the pristine rutile surface.

The size-modified Poisson-Boltzmann (MPB) equation is an efficient implicit solvation model which also captures electrolytic solvent effects. It combines an account of the dielectric solvent response with a mean-field description of solvated finite-sized ions. We present a general solution scheme for the MPB equation based on a fast function-space oriented Newton method and a Green's function preconditioned iterative linear solver. In contrast to popular multi-grid solvers this approach allows to fully exploit specialized integration grids and optimized integration schemes. We describe a corresponding numerically efficient implementation for the full-potential density-functional theory (DFT) code FHI-aims. We show that together with an additional Stern layer correction the DFT+MPB approach can describe the mean activity coefficient of a KCl aqueous solution over a wide range of concentrations. The high sensitivity of the calculated activity coefficient on the employed ionic parameters thereby suggests to use extensively tabulated experimental activity coefficients of salt solutions for a systematic parametrization protocol., Comment: Just accepted at Journal of Chemical Theory and Computation. This document is the unedited Authors version of a Submitted Work that was subsequently accepted for publication in the Journal of Chemical Theory and Computation, copyright American Chemical Society after peer review. To access the final edited and published work see http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00435

Efficient structure search is a major challenge in computational materials science. We present a modification of the basin hopping global geometry optimization approach that uses a curvilinear coordinate system to describe global trial moves. This approach has recently been shown to be efficient in structure determination of clusters [Nano Letters 15, 8044-8048 (2015)] and is here extended for its application to covalent, complex molecules and large adsorbates on surfaces. The employed, automatically constructed delocalized internal coordinates are similar to molecular vibrations, which enhances the generation of chemically meaningful trial structures. By introducing flexible constraints and local translation and rotation of independent geometrical subunits we enable the use of this method for molecules adsorbed on surfaces and interfaces. For two test systems, trans-$\beta$-ionylideneacetic acid adsorbed on a Au(111) surface and methane adsorbed on a Ag(111) surface, we obtain superior performance of the method compared to standard optimization moves based on Cartesian coordinates., Comment: 14 pages, 9 figures

The trans-cis isomerization makes azobenzene (AB) a robust molecular switch. Once adsorbed to a metal, however, the switching is inefficient or absent due to rapid excited-state quenching or loss of the trans-cis bistability. We find that tris-[4-(phenylazo)-phenyl]-amine is a rather efficient switch on Ag(111). Using scanning tunneling and atomic force microscopy at submolecular resolution along with density functional theory calculations, we show that the switching process is no trans-cis isomerization but rather a reorientation of the N-N bond of an AB unit. It proceeds through a twisting motion of the azo-bridge that leads to a lateral shift of a phenyl ring. Thus, the role of the Ag substrate is ambivalent. While it suppresses the original bistability of the azobenzene units, it creates a new one by inducing a barrier for the rotation of the N-N bond.

We introduce a system-independent method to derive effective atomic C$_6$ coefficients and polarizabilities in molecules and materials purely from charge population analysis. This enables the use of dispersion-correction schemes in electronic structure calculations without recourse to electron-density partitioning schemes and expands their applicability to semi-empirical methods and tight-binding Hamiltonians. We show that the accuracy of our method is en par with established electron-density partitioning based approaches in describing intermolecular C$_6$ coefficients as well as dispersion energies of weakly bound molecular dimers, organic crystals, and supramolecular complexes. We showcase the utility of our approach by incorporation of the recently developed many-body dispersion (MBD) method [Tkatchenko et al., Phys. Rev. Lett. 108, 236402 (2012)] into the semi-empirical Density Functional Tight-Binding (DFTB) method and propose the latter as a viable technique to study hybrid organic-inorganic interfaces., Comment: 5 pages, 2 figures, accepted for publication in J. Chem. Phys as a communication

Bifunctional coupling of two different catalytic site types has often been invoked to explain experimentally observed enhanced catalytic activities. We scrutinize such claims with generic scaling-relation-based microkinetic models that allow exploration of the theoretical limits for such a bifunctional gain for several model reactions. For sites at transition-metal surfaces, the universality of the scaling relations between adsorption energies largely prevents any improvements through bifunctionality. Only the consideration of systems that involve the combination of different materials, such as metal particles on oxide supports, offers hope for significant bifunctional gains.

We investigate transport effects in in situ studies of defined model catalysts using a multi-scale modeling approach integrating first-principles kinetic Monte Carlo simulations into a fluid dynamical treatment. We specifically address two isothermal flow setups: i) a channel flow with the gas-stream approaching the single crystal from the side, as is representative for reactor scanning tunneling microscopy experiments; and ii) a stagnation flow with perpendicular impingement. Using the CO oxidation at RuO2 (110) as showcase we obtain substantial variations in the gas-phase pressures between the inlet and the catalyst surface. In the channel geometry the mass transfer limitations lead furthermore to pronounced lateral changes in surface composition across the catalyst surface. This prevents the aspired direct relation between activity and catalyst structure. For the stagnation flow the lateral variations are restricted to the edges of the catalyst. This allows to access the desired structure-activity relation using a simple model., 22 pages, 7 figures

Forming the basis for the production of virtually all every-day products, catalysis has always been the driving force for chemical industries. In the 21st century, the concomitant importance of catalysis research is even further increased by the worldwide rapidly growing demand for more efficient exploitation of energy and materials resources. As in many other areas of materials science, modern computational science is becoming a key contributor in the quest to quantitatively understand the molecular-level mechanisms underlying the macroscopic phenomena in chemical processing, envisioned to ultimately enable a rational design of novel catalysts and improved production strategies. Of particular relevance are hierarchical approaches that link the insights that modeling and simulation can provide across all relevant length and time scales. At the molecular level, first-principles electronic-structure calculations unravel the making and breaking of chemical bonds. At the mesoscopic scale, statistical simulations account for the interplay between all elementary processes involved in the catalytic cycle, and at the macroscopic scale continuum theories yield the effect of heat and mass transfer, ultimately scaling up to a plant-wide simulation. A comprehensive control of catalytic processes requires to address all of these facets and will thus ultimately necessitate novel methodological approaches that integrate the various levels of theory into one multi-scale simulation. With the focus on the surface chemistry, first-principles kinetic Monte Carlo (kMC) simulations for heterogeneous catalysis represent precisely one step in this direction. A proper evaluation of the surface kinetics also dictates to unite two distinctly different aspects and in turn two distinct methodologies: The first important part is an accurate description of the involved elementary steps, typically comprising adsorption and desorption processes of reactants and reaction intermediates, as well as surface diffusion and surface reactions. When aiming at a material-specific modeling that is at best of predictive quality, the computation of the corresponding kinetic parameters is the realm of electronic structure theories that explicitly treat the electronic degrees of freedom and thus the quantum-mechanical nature of the chemical bond. Even though such a set of first-principles kinetic parameters constitutes already an (even for the most simple model systems hitherto barely achieved) important intermediate goal and highly valuable result, it does not suffice for a description of the surface catalytic function. For this, a second key ingredient is the occurrence (and thus relevance) of the individual elementary processes, in particular of the different reaction mechanisms. An evaluation of this statistical interplay within the manifold of elementary processes obviously needs to go beyond a separate study of each microscopic process. Taking the interplay into account naturally necessitates the treatment of larger surface areas. Much more challenging than this size, however, is the fact that the surface catalytic system is of course “open” in the sense that reactants, reaction intermediates and products continuously impinge from and desorb into the surrounding gas phase. Due to the highly activated nature of many of the involved elementary steps, the correspondingly required evaluation of the chemical kinetics faces the problem of a so-called “rare-event dynamics”, which means that the time between consecutive events can be orders of magnitude longer than the actual process time itself. Instead of the typical picosecond time scale on which say a surface diffusion event takes place, it may therefore be necessary to follow the time evolution of the system up to seconds and longer in order to arrive at meaningful conclusions concerning the statistical interplay.

We use Density-Functional Theory to investigate the structure and stability of a methylthiolate self-assembled monolayer (SAM) on Ag (1 1 1). Focusing on the role of substrate vacancies, we indeed find various structures with a reduced Ag-atom density in the outermost substrate layer that are significantly more stable than an unreconstructed SAM/substrate interface. The most stable structure exhibits a very small rumpling of the methylthiolate layer and a mean height of the anchoring S atoms above the surface that are both in excellent agreement with experiment. Previously reported discrepancies thus result from an insufficient configurational screening.

The conceptual idea of degree of rate control (DRC) approaches is to identify the "rate limiting step" in a complex reaction network by evaluating how the overall rate of product formation changes when a small change is made in one of the kinetic parameters. We examine two definitions of this concept by applying it to first-principles kinetic Monte Carlo simulations of the CO oxidation at RuO2(110). Instead of studying experimental data we examine simulations, because in them we know the surface structure, reaction mechanism, the rate constants, the coverage of the surface and the turn-over frequency at steady state. We can test whether the insights provided by the DRC are in agreement with the results of the simulations thus avoiding the uncertainties inherent in a comparison with experiment. We find that the information provided by using the DRC is non-trivial: It could not have been obtained from the knowledge of the reaction mechanism and of the magnitude of the rate constants alone. For the simulations the DRC provides furthermore guidance as to which aspects of the reaction mechanism should be treated accurately and which can be studied by less accurate and more efficient methods. We therefore conclude that a sensitivity analysis based on the DRC is a useful tool for understanding the propagation of errors from the electronic structure calculations to the statistical simulations in first-principles kinetic Monte Carlo simulations., Comment: 27 pages including 5 figures; related publications can be found at http://www.fhi-berlin.mpg.de/th/th.html

We return to the geometry optimization problem of Lennard-Jones clusters to analyze the performance dependence of "cut and splice" genetic algorithms (GAs) on the employed population size. We generally find that admixing twinning mutation moves leads to an improved robustness of the algorithm efficiency with respect to this a priori unknown technical parameter. The resulting very stable performance of the corresponding mutation+mating GA implementation over a wide range of population sizes is an important feature when addressing unknown systems with computationally involved first-principles based GA sampling., Comment: 5 pages including 3 figures; related publications can be found at http://www.fhi-berlin.mpg.de/th/th.html

A parallel implementation of a nonlinear pseudo-spectral MHD code for the simulation of turbulent dynamos in spherical geometry is reported. It employs a dual domain decomposition technique in both real and spectral space. It is shown that this method shows nearly ideal scaling going up to 128 CPUs on Beowulf-type clusters with fast interconnect. Furthermore, the potential of exploiting single precision arithmetic on standard x86 processors is examined. It is pointed out that the MHD code thereby achieves a maximum speedup of 1.7, whereas the validity of the computations is still granted. The combination of both measures will allow for the direct numerical simulation of highly turbulent cases (1500 < Re < 5000), which have been previously impractical, given today’s computational speed. © 2008 Elsevier B.V. All rights reserved.

All-trans-retinoic acid (ReA), a closed-shell organic molecule comprising only C, H, and O atoms, is investigated on a Au(111) substrate using scanning tunneling microscopy and spectroscopy. In dense arrays single ReA molecules are switched to a number of states, three of which carry a localized spin as evidenced by conductance spectroscopy in high magnetic fields. The spin of a single molecule may be reversibly switched on and off without affecting its neighbors. We suggest that ReA on Au is readily converted to a radical by the abstraction of an electron., 5 pages, 3 figures, accepted for publication in Phys. Rev. Lett

We investigate the thermal and electronic collective fluctuations that contribute to the finite-temperature adsorption properties of flexible adsorbates on surfaces on the example of the molecular switch azobenzene C$_{12}$H$_{10}$N$_{2}$ on the Ag(111) surface. Using first-principles molecular dynamics simulations we obtain the free energy of adsorption that accurately accounts for entropic contributions, whereas the inclusion of many-body dispersion interactions accounts for the electronic correlations that govern the adsorbate binding. We find the adsorbate properties to be strongly entropy-driven, as can be judged by a kinetic molecular desorption prefactor of 10$^{24}$ s$^{-1}$ that largely exceeds previously reported estimates. We relate this effect to sizable fluctuations across structural and electronic observables. Comparison of our calculations to temperature-programmed desorption measurements demonstrates that finite-temperature effects play a dominant role for flexible molecules in contact with polarizable surfaces, and that recently developed first-principles methods offer an optimal tool to reveal novel collective behavior in such complex systems., Comment: 6 pages, 3 figures, accepted for publication in Phys. Rev. Lett

The elementary reactions leading to the formation of the first carbon-carbon bond during early stages of the zeolite-catalyzed methanol conversion into hydrocarbons were identified by combining kinetics, spectroscopy, and DFT calculations. The first intermediates containing a C-C bond are acetic acid and methyl acetate, which are formed through carbonylation of methanol or dimethyl ether even in presence of water. A series of acid-catalyzed reactions including acetylation, decarboxylation, aldol condensation, and cracking convert those intermediates into a mixture of surface bounded hydrocarbons, the hydrocarbon pool, as well as into the first olefin leaving the catalyst. This carbonylation based mechanism has an energy barrier of 80 kJ mol(-1) for the formation of the first C-C bond, in line with a broad range of experiments, and significantly lower than the barriers associated with earlier proposed mechanisms.

Identification of relevant reaction pathways in ever more complex composite materials and nanostructures poses a central challenge to computational materials discovery. Efficient global structure search, tailored to identify chemically relevant intermediates, could provide the necessary first-principles atomistic insight to enable a rational process design. In this work we modify a common feature of global geometry optimization schemes by employing automatically generated collective curvilinear coordinates. The similarity of these coordinates to molecular vibrations enhances the generation of chemically meaningful trial structures for covalently bound systems. In the application to hydrogenated Si clusters, we concomitantly observe a significantly increased efficiency in identifying low-energy structures and exploit it for an extensive sampling of potential products of silicon-cluster soft landing on Si(001) surfaces.

We present a critical analysis of the popular fragment-orbital density-functional theory (FO-DFT) scheme for the calculation of electronic coupling values. We discuss the characteristics of different possible formulations or “flavors” of the scheme which differ by the number of electrons in the calculation of the fragments and the construction of the Hamiltonian. In addition to two previously described variants based on neutral fragments, we present a third version taking a different route to the approximate diabatic state by explicitly considering charged fragments. In applying these FO-DFT flavors to the two molecular test sets HAB7 (electron transfer) and HAB11 (hole transfer), we find that our new scheme gives improved electronic couplings for HAB7 (−6.2% decrease in mean relative signed error) and greatly improved electronic couplings for HAB11 (−15.3% decrease in mean relative signed error). A systematic investigation of the influence of exact exchange on the electronic coupling values shows that the use of hybrid functionals in FO-DFT calculations improves the electronic couplings, giving values close to or even better than more sophisticated constrained DFT calculations. Comparing the accuracy and computational cost of each variant, we devise simple rules to choose the best possible flavor depending on the task. For accuracy, our new scheme with charged-fragment calculations performs best, while numerically more efficient at reasonable accuracy is the variant with neutral fragments.

Bisphenol A (BPA) aggregates on Ag(111) shows a polymorphism between two supramolecular motifs leading to formation of distinct networks depending on thermal energy. With rising temperature a dimeric pairing scheme reversibly converts into a trimeric motif, which forms a hexagonal superstructure with complex dynamic characteristics. The trimeric arrangements notably organize spontaneously into a self-assembled one-component array with supramolecular BPA rotors embedded in a two-dimensional stator sublattice. By varying the temperature, the speed of the rotors can be controlled as monitored by direct visualization. A combination of scanning tunneling microscopy and dispersion-corrected density-functional tight-binding (DFTB-vdW(surf)) based molecular modeling reveals the exact atomistic position of each molecule within the assembly as well as the driving force for the formation of the supramolecular rotors.

We investigate the surface-catalyzed dissociation of the archetypal molecular switch azobenzene on the Cu(111) surface. Based on X-ray photoelectron spectroscopy, normal incidence X-ray standing waves and density functional theory calculations a detailed picture of the coverage-induced formation of phenyl nitrene from azobenzene is presented. Furthermore, a comparison to the azobenzene/Ag(111) interface provides insight into the driving force behind the dissociation on Cu(111). The quantitative decay of azobenzene paves the way for the creation of a defect free, covalently bonded monolayer. Our work suggests a route of surface functionalization via suitable azobenzene derivatives and the on surface synthesis concept, allowing for the creation of complex immobilized molecular systems.