arXiv subjects

Karsten Reuter

Publications and source records attributed to Karsten Reuter.

At least 55 records · Page 3Linked to original sources

arXiv2019

Efficient Simulation of Near-Edge X-ray Absorption Fine Structure (NEXAFS) in Density-Functional Theory: Comparison of Core-Level Constraining Approaches

Widely employed Near-Edge X-Ray Absorption Fine Structure (NEXAFS) spectroscopy probes a system by excitation of core electrons to unoccupied states. A variety of different methodologies are available to simulate corresponding spectra from first-principles. Core-level occupation constraints within ground-state Density-Functional Theory (DFT) represent a numerically most efficient means to this end that provides access to large systems, examples being surface adsorption, proteins, polymers, liquids, and buried, condensed phase interfaces (e.q. solid-liquid and solid-solid). Here, we systematically investigate the performance of different realizations of this approximate approach through the simulation of K-edge NEXAFS-spectra of a set of carbon and nitrogen-containing organic molecules. Variational collapse to the ground state and oscillatory convergence are the major complications of these approximate computational protocols. We present a modified version of the maximum-overlap method to achieve a self-consistent inclusion of electrons in virtual states for systems where convergence is hampered due to degeneracies. Our results demonstrate that reliable spectra allowing for a semi-quantitative analysis of experimental data are already obtained at the semi-local level of density functionals and with standard numeric atomic orbital basis sets.

physics.chem-ph↗

arXiv2018

Computational design of metal-supported molecular switches: Transient ion formation during light- and electron-induced isomerisation of azobenzene

In molecular nanotechnology, a single molecule is envisioned to act as the basic building block of electronic devices. Such devices may be of special interest for organic photovoltaics, data storage, and smart materials. However, more often than not the molecular function is quenched upon contact with a conducting support. Trial-and-error-based decoupling strategies via molecular functionalisation and change of substrate have in many instances proven to yield unpredictable results. The adsorbate-substrate interactions that govern the function can be understood with the help of first-principles simulation. Employing dispersion-corrected Density-Functional Theory (DFT) and linear expansion Delta-Self-Consistent-Field DFT, the electronic structure of a prototypical surface-adsorbed functional molecule, namely azobenzene adsorbed to (111) single crystal facets of copper, silver and gold, is investigated and the main reasons for the loss or survival of the switching function upon adsorption are identified. The light-induced switching ability of a functionalised derivative of azobenzene on Au(111) and azobenzene on Ag(111) and Au(111) is assessed based on the excited-state potential energy landscapes of their transient molecular ions, which are believed to be the main intermediates of the experimentally observed isomerisation reaction. We provide a rationalisation of the experimentally observed function or lack thereof that connects to the underlying chemistry of the metal-surface interaction and provides insights into general design strategies for complex light-driven reactions at metal surfaces.

cond-mat.mtrl-sci↗

arXiv2018

Benefits from using mixed precision computations in the ELPA-AEO and ESSEX-II eigensolver projects

We first briefly report on the status and recent achievements of the ELPA-AEO (Eigenvalue Solvers for Petaflop Applications - Algorithmic Extensions and Optimizations) and ESSEX II (Equipping Sparse Solvers for Exascale) projects. In both collaboratory efforts, scientists from the application areas, mathematicians, and computer scientists work together to develop and make available efficient highly parallel methods for the solution of eigenvalue problems. Then we focus on a topic addressed in both projects, the use of mixed precision computations to enhance efficiency. We give a more detailed description of our approaches for benefiting from either lower or higher precision in three selected contexts and of the results thus obtained.

physics.comp-ph↗

arXiv2018

Genarris: Random Generation of Molecular Crystal Structures and Fast Screening with a Harris Approximation

We present Genarris, a Python package that performs configuration space screening for molecular crystals of rigid molecules by random sampling with physical constraints. For fast energy evaluations Genarris employs a Harris approximation, whereby the total density of a molecular crystal is constructed via superposition of single molecule densities. Dispersion-inclusive density functional theory (DFT) is then used for the Harris density without performing a self-consistency cycle. Genarris uses machine learning for clustering, based on a relative coordinate descriptor (RCD) developed specifically for molecular crystals, which is shown to be robust in identifying packing motif similarity. In addition to random structure generation, Genarris offers three workflows based on different sequences of successive clustering and selection steps: the "Rigorous" workflow is an exhaustive exploration of the potential energy landscape, the "Energy" workflow produces a set of low energy structures, and the "Diverse" workflow produces a maximally diverse set of structures. The latter is recommended for generating initial populations for genetic algorithms. Here, the implementation of Genarris is reported and its application is demonstrated for three test cases.

physics.comp-ph↗

arXiv2017

Non-Adiabatic Vibrational Damping of Molecular Adsorbates: Insights into Electronic Friction and the Role of Electronic Coherence

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.

physics.chem-ph↗

arXiv2017

Theoretical evidence for unexpected O-rich phases at corners of MgO surfaces

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.

cond-mat.mtrl-sci↗

arXiv2017

Interpretation of X-ray Absorption Spectroscopy in the Presence of Surface Hybridization

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.

physics.chem-ph↗

arXiv2016

Energy Dissipation during Diffusion at Metal Surfaces: Disentangling the Role of Phonons vs. Electron-Hole Pairs

Helium spin echo experiments combined with ab initio-based Langevin molecular dynamics simulations are used to quantify the adsorbate-substrate coupling during the thermal diffusion of Na atoms on Cu(111). An analysis of trajectories within the local density friction approximation allows the contribution from electron-hole pair excitations to be separated from the total energy dissipation. Despite the minimal electronic friction coefficient of Na and the relatively small mass mismatch to Cu promoting efficient phononic dissipation, about $(20\pm5)\%$ of the total energy loss is attributable to electronic friction. The results suggest a significant role of electronic non-adiabaticity in the rapid thermalization generally relied upon in adiabatic diffusion theories.

cond-mat.mtrl-sci↗

arXiv2016

Global Structure Search for Molecules on Surfaces: Efficient Sampling with Curvilinear Coordinates

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-$β$-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.

cond-mat.mtrl-sci↗

arXiv2016

Function-Space Based Solution Scheme for the Size-Modified Poisson-Boltzmann Equation in Full-Potential DFT

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.

cond-mat.mtrl-sci↗

arXiv2016

Adsorption structures and energetics of molecules on metal surfaces: Bridging experiment and theory

Adsorption geometry and stability of organic molecules on surfaces are key parameters that determine the observable properties and functions of hybrid inorganic/organic systems (HIOSs). Despite many recent advances in precise experimental characterization and improvements in first-principles electronic structure methods, reliable databases of structures and energetics for large adsorbed molecules are largely amiss. In this review, we present such a database for a range of molecules adsorbed on metal single-crystal surfaces. The systems we analyze include noble-gas atoms, conjugated aromatic molecules, carbon nanostructures, and heteroaromatic compounds adsorbed on five different metal surfaces. The overall objective is to establish a diverse benchmark dataset that enables an assessment of current and future electronic structure methods, and motivates further experimental studies that provide ever more reliable data. Specifically, the benchmark structures and energetics from experiment are here compared with the recently developed van der Waals (vdW) inclusive density-functional theory (DFT) method, DFT+vdW$^{\mathrm{surf}}$. In comparison to 23 adsorption heights and 17 adsorption energies from experiment we find a mean average deviation of 0.06 Å and 0.16 eV, respectively. This confirms the DFT+vdW$^{\mathrm{surf}}$ method as an accurate and efficient approach to treat HIOSs. A detailed discussion identifies remaining challenges to be addressed in future development of electronic structure methods, for which the here presented benchmark database may serve as an important reference.

cond-mat.mtrl-sci↗

arXiv2016

Communication: Charge-Population Based Dispersion Interactions for Molecules and Materials

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.

cond-mat.mtrl-sci↗

arXiv2016

Thermal and electronic fluctuations of flexible adsorbed molecules: Azobenzene on Ag(111)

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.

cond-mat.mtrl-sci↗

arXiv2015

Spin Manipulation by Creation of Single-Molecule Radical Cations

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.

cond-mat.mtrl-sci↗

arXiv2015

Interfacial charge rearrangement and intermolecular interactions: Density-functional theory study of free-base porphine adsorbed on Ag(111) and Cu(111)

We employ dispersion-corrected density-functional theory to study the adsorption of tetrapyrrole 2H-porphine (2H-P) at Cu(111) and Ag(111). Various contributions to adsorbate-substrate and adsorbate-adsorbate interactions are systematically extracted to analyze the self-assembly behavior of this basic building block to porphyrin-based metal-organic nanostructures. This analysis reveals a surprising importance of substrate-mediated van der Waals interactions between 2H-P molecules, in contrast to negligible direct dispersive interactions. The resulting net repulsive interactions rationalize the experimentally observed tendency for single molecule adsorption.

physics.chem-ph↗

arXiv2015

Critical analysis of fragment-orbital DFT schemes for the calculation of electronic coupling values

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.

cond-mat.mtrl-sci↗

arXiv2015

Structure Sensitivity in Oxide Catalysis: First-Principles Kinetic Monte Carlo Simulations for CO Oxidation at RuO$_2$(111)

We present a density-functional theory based kinetic Monte Carlo study of CO oxidation at the (111) facet of RuO$_2$. We compare the detailed insight into elementary processes, steady-state surface coverages and catalytic activity to equivalent published simulation data for the frequently studied RuO$_2$(110) facet. Qualitative differences are identified in virtually every aspect ranging from binding energetics over lateral interactions to the interplay of elementary processes at the different active sites. Nevertheless, particularly at technologically relevant elevated temperatures, near-ambient pressures and near-stoichiometric feeds both facets exhibit almost identical catalytic activity. These findings challenge the traditional definition of structure sensitivity based on macroscopically observable turnover frequencies and allow to scrutinize the applicability of structure sensitivity classifications developed for metals to oxide catalysis.

cond-mat.mtrl-sci↗

arXiv2015

Electronic friction-based vibrational lifetimes of molecular adsorbates: Beyond the independent atom approximation

We assess the accuracy of vibrational damping rates of diatomic adsorbates on metal surfaces as calculated within the local-density friction approximation (LDFA). An atoms-in-molecules (AIM) type charge partitioning scheme accounts for intra-molecular contributions and overcomes the systematic underestimation of the non-adiabatic losses obtained within the prevalent independent atom approximation. The quantitative agreement obtained with theoretical and experimental benchmark data suggests the LDFA-AIM as an efficient and reliable approach to account for electronic dissipation in ab initio molecular dynamics simulations of surface chemical reactions.

cond-mat.mtrl-sci↗