Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method

Band structure engineered layered metals for low-loss plasmonics

Plasmonics currently faces the problem of seemingly inevitable optical losses occurring in the metallic components that challenges the implementation of essentially any application. In this work, we show that Ohmic losses are reduced in certain layered metals, such as the transition metal dichalcogenide TaS₂, due to an extraordinarily small density of states for scattering in the near-IR originating from their special electronic band structure. On the basis of this observation, we propose a new class of band structure engineered van der Waals layered metals composed of hexagonal transition metal chalcogenide-halide layers with greatly suppressed intrinsic losses. Using first-principles calculations, we show that the suppression of optical losses lead to improved performance for thin-film waveguiding and transformation optics.

High Redox Capacity of Al-Doped La1-x Srx MnO3-δ Perovskites for Splitting CO2 and H2 O at Mn-Enriched Surfaces

Perovskites are attractive candidates for the solar-driven thermochemical redox splitting of CO₂ and H₂ O into CO and H₂ (syngas) and O₂ . This work investigates the surface activity of La_1-x Sr_x Mn_1-y Al_y O_3-δ (0≤x≤1, 0≤y≤1) and La_0.6 Ca_0.4 Mn_0.6 Al_0.4 O_3-δ . At 1623 K and 15 mbar O₂ , the oxygen non-stoichiometry of La_0.2 Sr_0.8 Mn_0.8 Al_0.2 O_3-δ increases with the strontium content and reaches a maximum of δ=0.351. X-ray photoelectron spectroscopy analysis indicates that manganese is the only redox-active metal at the surface. All La_1-x Sr_x Mn_1-y Al_y O_3-δ compositions exhibit surfaces enriched in manganese and depleted in strontium. We discuss how these compositional differences of the surface from the bulk lead to the beneficially higher reduction extents and lower strontium carbonate concentrations at the aluminum-doped surfaces. Using first principles calculations, we validate the experimental reduction trends and elucidate the mechanism of the partial electronic charge redistribution upon perovskite reduction.

First-Principles Study of the Band Diagrams and Schottky-Type Barrier Heights of Aqueous Ta3N5 Interfaces

The photo(electro)chemical production of hydrogen by water splitting is an efficient and sustainable method for the utilization of solar energy. To improve photo(electro)catalytic activity, a Schottky-type barrier is typically useful to separate excited charge carriers in semiconductor electrodes. Here, we focused on studying the band diagrams and the Schottky-type barrier heights of Ta₃N₅, which is one of the most promising materials as a photoanode for water splitting. The band alignments of the undoped and n-type Ta₃N₅ with adsorbents in a vacuum were examined to determine how impurities and adsorbents affect the band positions and Fermi energies. The band edge positions as well as the density of surface states clearly depended on the density of O_N impurities in the bulk and surface regions. Finally, the band diagrams of the n-type Ta₃N₅/water interfaces were calculated with an improved interfacial model to include the effect of electrode potential with explicit water molecules. We observed partial Fermi level pinning in our calculations at the Ta₃N₅/water interface, which affects the driving force for charge separation.

Quantitative and Atomic-Scale View of CO-Induced Pt Nanoparticle Surface Reconstruction at Saturation Coverage via DFT Calculations Coupled with in Situ TEM and IR

Atomic-scale insights into how supported metal nanoparticles catalyze chemical reactions are critical for the optimization of chemical conversion processes. It is well-known that different geometric configurations of surface atoms on supported metal nanoparticles have different catalytic reactivity and that the adsorption of reactive species can cause reconstruction of metal surfaces. Thus, characterizing metallic surface structures under reaction conditions at atomic scale is critical for understanding reactivity. Elucidation of such insights on high surface area oxide supported metal nanoparticles has been limited by less than atomic resolution typically achieved by environmental transmission electron microscopy (TEM) when operated under realistic conditions and a lack of correlated experimental measurements providing quantitative information about the distribution of exposed surface atoms under relevant reaction conditions. We overcome these limitations by correlating density functional theory predictions of adsorbate-induced surface reconstruction visually with atom-resolved imaging by in situ TEM and quantitatively with sample-averaged measurements of surface atom configurations by in situ infrared spectroscopy all at identical saturation adsorbate coverage. This is demonstrated for platinum (Pt) nanoparticle surface reconstruction induced by CO adsorption at saturation coverage and elevated (>400 K) temperature, which is relevant for the CO oxidation reaction under cold-start conditions in the catalytic convertor. Through our correlated approach, it is observed that the truncated octahedron shape adopted by bare Pt nanoparticles undergoes a reversible, facet selective reconstruction due to saturation CO coverage, where {100} facets roughen into vicinal stepped high Miller index facets, while {111} facets remain intact.

Stabilization of the Perovskite Phase of Formamidinium Lead Triiodide by Methylammonium, Cs, and/or Rb Doping

In this work we perform a computational study comparing the influence of monovalent cation substitution by methylammonium (MA⁺), cesium (Cs⁺), and rubidium (Rb⁺) on the properties of formamidinium lead triiodide (FAPbI₃)-based perovskites. The relative stability of the desired, photoactive perovskite α phase ("black phase") and the nonphotoactive, nonperovskite δ phase ("yellow phase") is studied as a function of dopant nature, concentration and temperature. Cs⁺ and Rb⁺ are shown to be more efficient in the stabilization of the perovskite α phase than MA⁺. Furthermore, varying the dopant concentration allows changing the relative stability at different temperatures, in particular stabilizing the α phase already at 200 K. Upon Cs⁺ or Rb⁺ doping, the corresponding onset of the optical spectrum is blue-shifted by 0.1-0.2 eV with respect to pure FAPbI₃.

Self-energy matrices for electron transport calculations within the real-space finite-difference formalism

The self-energy term used in transport calculations, which describes the coupling between electrode and transition regions, is able to be evaluated only from a limited number of the propagating and evanescent waves of a bulk electrode. This obviously contributes toward the reduction of the computational expenses in transport calculations. In this paper, we present a mathematical formula for reducing the computational expenses further without using any approximation and without losing accuracy. So far, the self-energy term has been handled as a matrix with the same dimension as the Hamiltonian submatrix representing the interaction between an electrode and a transition region. In this work, through the singular-value decomposition of the submatrix, the self-energy matrix is handled as a smaller matrix, whose dimension is the rank number of the Hamiltonian submatrix. This procedure is practical in the case of using the pseudopotentials in a separable form, and the computational expenses for determining the self-energy matrix are reduced by 90% when employing a code based on the real-space finite-difference formalism and projector-augmented wave method. In addition, this technique is applicable to the transport calculations using atomic or localized basis sets. Adopting the self-energy matrices obtained from this procedure, we present the calculation of the electron transport properties of C_{20} molecular junctions. The application demonstrates that the electron transmissions are sensitive to the orientation of the molecule with respect to the electrode surface. In addition, channel decomposition of the scattering wave functions reveals that some unoccupied C_{20} molecular orbitals mainly contribute to the electron conduction through the molecular junction.

A Generalized Grid-Based Fast Multipole Method for Integrating Helmholtz Kernels

A grid-based fast multipole method (GB-FMM) for optimizing three-dimensional (3D) numerical molecular orbitals in the bubbles and cube double basis has been developed and implemented. The present GB-FMM method is a generalization of our recently published GB-FMM approach for numerically calculating electrostatic potentials and two-electron interaction energies. The orbital optimization is performed by integrating the Helmholtz kernel in the double basis. The steep part of the functions in the vicinity of the nuclei is represented by one-center bubbles functions, whereas the remaining cube part is expanded on an equidistant 3D grid. The integration of the bubbles part is treated by using one-center expansions of the Helmholtz kernel in spherical harmonics multiplied with modified spherical Bessel functions of the first and second kind, analogously to the numerical inward and outward integration approach for calculating two-electron interaction potentials in atomic structure calculations. The expressions and algorithms for massively parallel calculations on general purpose graphics processing units (GPGPU) are described. The accuracy and the correctness of the implementation has been checked by performing Hartree-Fock self-consistent-field calculations (HF-SCF) on H₂, H₂O, and CO. Our calculations show that an accuracy of 10^-4 to 10^-7 E_h can be reached in HF-SCF calculations on general molecules.

Colorimetric gas detection by the varying thickness of a thin film of ultrasmall PTSA-coated TiO2 nanoparticles on a Si substrate

Colorimetric gas sensing is demonstrated by thin films based on ultrasmall TiO₂ nanoparticles (NPs) on Si substrates. The NPs are bound into the film by p-toluenesulfonic acid (PTSA) and the film is made to absorb volatile organic compounds (VOCs). Since the color of the sensing element depends on the interference of reflected light from the surface of the film and from the film/silicon substrate interface, colorimetric detection is possible by the varying thickness of the NP-based film. Indeed, VOC absorption causes significant swelling of the film. Thus, the optical path length is increased, interference wavelengths are shifted and the refractive index of the film is decreased. This causes a change of color of the sensor element visible by the naked eye. The color response is rapid and changes reversibly within seconds of exposure. The sensing element is extremely simple and cheap, and can be fabricated by common coating processes.

Orbitalwise Coordination Number for Predicting Adsorption Properties of Metal Nanocatalysts

We present the orbitalwise coordination number CN^{α} (α=s or d) as a reactivity descriptor for metal nanocatalysts. With the noble metal Au (5d^{10}6s^{1}) as a specific case, the CN^{s} computed using the two-center s-electron hopping integrals to neighboring atoms provides an accurate and robust description of the trends in CO and O adsorption energies on extended surfaces terminated with different facets and nanoparticles of varying size and shape, outperforming existing bond-counting methods. Importantly, the CN^{s} has a solid physiochemical basis via a direct connection to the moment characteristics of the projected density of states onto the s orbital of a Au adsorption site. Furthermore, the CN^{s} shows promise as a viable descriptor for predicting adsorption properties of Au alloy nanoparticles with size-dependent lattice strains and coinage metal ligands.

Symmetry-Driven Band Gap Engineering in Hydrogen Functionalized Graphene

Band gap engineering in hydrogen functionalized graphene is demonstrated by changing the symmetry of the functionalization structures. Small differences in hydrogen adsorbate binding energies on graphene on Ir(111) allow tailoring of highly periodic functionalization structures favoring one distinct region of the moiré supercell. Scanning tunneling microscopy and X-ray photoelectron spectroscopy measurements show that a highly periodic hydrogen functionalized graphene sheet can thus be prepared by controlling the sample temperature (T_s) during hydrogen functionalization. At deposition temperatures of T_s = 645 K and above, hydrogen adsorbs exclusively on the HCP regions of the graphene/Ir(111) moiré structure. This finding is rationalized in terms of a slight preference for hydrogen clusters in the HCP regions over the FCC regions, as found by density functional theory calculations. Angle-resolved photoemission spectroscopy measurements demonstrate that the preferential functionalization of just one region of the moiré supercell results in a band gap opening with very limited associated band broadening. Thus, hydrogenation at elevated sample temperatures provides a pathway to efficient band gap engineering in graphene via the selective functionalization of specific regions of the moiré structure.

Tomography of a Probe Potential Using Atomic Sensors on Graphene

Our ability to access and explore the quantum world has been greatly advanced by the power of atomic manipulation and local spectroscopy with scanning tunneling and atomic force microscopes, where the key technique is the use of atomically sharp probe tips to interact with an underlying substrate. Here we employ atomic manipulation to modify and quantify the interaction between the probe and the system under study that can strongly affect any measurement in low charge density systems, such as graphene. We transfer Co atoms from a graphene surface onto a probe tip to change and control the probe's physical structure, enabling us to modify the induced potential at a graphene surface. We utilize single Co atoms on a graphene field-effect device as atomic scale sensors to quantitatively map the modified potential exerted by the scanning probe over the whole relevant spatial and energy range.

Single Crystal Sub-Nanometer Sized Cu6(SR)6 Clusters: Structure, Photophysical Properties, and Electrochemical Sensing

Organic ligand-protected metal nanoclusters have attracted extensively attention owing to their atomically precise composition, determined atom-packing structure and the fascinating properties and promising applications. To date, most research has been focused on thiol-stabilized gold and silver nanoclusters and their single crystal structures. Here the single crystal copper nanocluster species (Cu6(SC7H4NO)6) determined by X-ray crystallography and mass spectrometry is presented. The hexanuclear copper core is a distorted octahedron surrounded by six mercaptobenzoxazole ligands as protecting units through a simple bridging bonding motif. Density functional theory (DFT) calculations provide insight into the electronic structure and show the cluster can be viewed as an open-shell nanocluster. The UV-vis spectra are analyzed using time-dependent DFT and illustrates high-intensity transitions involving primarily ligand states. Furthermore, the as-synthesized copper clusters can serve as promising nonenzymatic sensing materials for high sensitive and selective detection of H2O2.

Structure-conserving spontaneous transformations between nanoparticles

Ambient, structure- and topology-preserving chemical reactions between two archetypal nanoparticles, Ag₂₅(SR)₁₈ and Au₂₅(SR)₁₈, are presented. Despite their geometric robustness and electronic stability, reactions between them in solution produce alloys, Ag_mAu_n(SR)₁₈ (m+n=25), keeping their M₂₅(SR)₁₈ composition, structure and topology intact. We demonstrate that a mixture of Ag₂₅(SR)₁₈ and Au₂₅(SR)₁₈ can be transformed to any arbitrary alloy composition, Ag_mAu_n(SR)₁₈ (n=1-24), merely by controlling the reactant compositions. We capture one of the earliest events of the process, namely the formation of the dianionic adduct, (Ag₂₅Au₂₅(SR)₃₆)^2-, by electrospray ionization mass spectrometry. Molecular docking simulations and density functional theory (DFT) calculations also suggest that metal atom exchanges occur through the formation of an adduct between the two clusters. DFT calculations further confirm that metal atom exchanges are thermodynamically feasible. Such isomorphous transformations between nanoparticles imply that microscopic pieces of matter can be transformed completely to chemically different entities, preserving their structures, at least in the nanometric regime.

The influence of coronene super-hydrogenation on the coronene-graphite interaction

The changes in the strength of the interaction between the polycyclic aromatic hydrocarbon, coronene, and graphite as a function of the degree of super-hydrogenation of the coronene molecule are investigated using temperature programmed desorption. A decrease in binding energy is observed for increasing degrees of super-hydrogenation, from 1.78 eV with no additional hydrogenation to 1.43 eV for the fully super-hydrogenated molecule. Density functional theory calculations using the optB88-vdW functional suggest that the decrease in binding energy is mostly due to an increased buckling of the molecule rather than the associated decrease in the number of π-electrons.

Band Gap Tuning and Defect Tolerance of Atomically Thin Two-Dimensional Organic-Inorganic Halide Perovskites

Organic-inorganic halide perovskites have proven highly successful for photovoltaics but suffer from low stability, which deteriorates their performance over time. Recent experiments have demonstrated that low dimensional phases of the hybrid perovskites may exhibit improved stability. Here we report first-principles calculations for isolated monolayers of the organometallic halide perovskites (C₄H₉NH₃)₂MX₂Y₂, where M = Pb, Ge, Sn and X,Y = Cl, Br, I. The band gaps computed using the GLLB-SC functional are found to be in excellent agreement with experimental photoluminescence data for the already synthesized perovskites. Finally, we study the effect of different defects on the band structure. We find that the most common defects only introduce shallow or no states in the band gap, indicating that these atomically thin 2D perovskites are likely to be defect tolerant.

Spectromicroscopy of C60 and azafullerene C59N: Identifying surface adsorbed water

C60 fullerene crystals may serve as important catalysts for interstellar organic chemistry. To explore this possibility, the electronic structures of free-standing powders of C60 and (C59N)2 azafullerenes are characterized using X-ray microscopy with near-edge X-ray adsorption fine structure (NEXAFS) spectroscopy, closely coupled with density functional theory (DFT) calculations. This is supported with X-ray photoelectron spectroscopy (XPS) measurements and associated core-level shift DFT calculations. We compare the oxygen 1s spectra from oxygen impurities in C60 and C59N, and calculate a range of possible oxidized and hydroxylated structures and associated formation barriers. These results allow us to propose a model for the oxygen present in these samples, notably the importance of water surface adsorption and possible ice formation. Water adsorption on C60 crystal surfaces may prove important for astrobiological studies of interstellar amino acid formation.

Isotope analysis in the transmission electron microscope

The Ångström-sized probe of the scanning transmission electron microscope can visualize and collect spectra from single atoms. This can unambiguously resolve the chemical structure of materials, but not their isotopic composition. Here we differentiate between two isotopes of the same element by quantifying how likely the energetic imaging electrons are to eject atoms. First, we measure the displacement probability in graphene grown from either ¹²C or ¹³C and describe the process using a quantum mechanical model of lattice vibrations coupled with density functional theory simulations. We then test our spatial resolution in a mixed sample by ejecting individual atoms from nanoscale areas spanning an interface region that is far from atomically sharp, mapping the isotope concentration with a precision better than 20%. Although we use a scanning instrument, our method may be applicable to any atomic resolution transmission electron microscope and to other low-dimensional materials.

Applications of large-scale density functional theory in biology

Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.

Chemical Bond Activation Observed with an X-ray Laser

The concept of bonding and antibonding orbitals is fundamental in chemistry. The population of those orbitals and the energetic difference between the two reflect the strength of the bonding interaction. Weakening the bond is expected to reduce this energetic splitting, but the transient character of bond-activation has so far prohibited direct experimental access. Here we apply time-resolved soft X-ray spectroscopy at a free-electron laser to directly observe the decreased bonding-antibonding splitting following bond-activation using an ultrashort optical laser pulse.

Plasmonic twinned silver nanoparticles with molecular precision

Determining the structures of nanoparticles at atomic resolution is vital to understand their structure–property correlations. Large metal nanoparticles with core diameter beyond 2 nm have, to date, eluded characterization by single-crystal X-ray analysis. Here we report the chemical syntheses and structures of two giant thiolated Ag nanoparticles containing 136 and 374 Ag atoms (that is, up to 3 nm core diameter). As the largest thiolated metal nanoparticles crystallographically determined so far, these Ag nanoparticles enter the truly metallic regime with the emergence of surface plasmon resonance. As miniatures of fivefold twinned nanostructures, these structures demonstrate a subtle distortion within fivefold twinned nanostructures of face-centred cubic metals. The Ag nanoparticles reported in this work serve as excellent models to understand the detailed structure distortion within twinned metal nanostructures and also how silver nanoparticles can span from the molecular to the metallic regime.

The structure of nanoparticles strongly influences their properties. Here, the authors use single crystal X-ray diffraction to resolve the crystal structures of Ag₁₃₆ and Ag₃₇₄ nanoparticles, enabling the observation of local structure distortion and the lower size limit of surface plasmon resonance.

Thermodynamic Insight in the High-Pressure Behavior of UiO-66: Effect of Linker Defects and Linker Expansion

In this Article, we present a molecular-level understanding of the experimentally observed loss of crystallinity in UiO-66-type metal-organic frameworks, including the pristine UiO-66 to -68 as well as defect-containing UiO-66 materials, under the influence of external pressure. This goal is achieved by constructing pressure-versus-volume profiles at finite temperatures using a thermodynamic approach relying on ab initio derived force fields. On the atomic level, the phenomenon is reflected in a sudden drop in the number of symmetry operators for the crystallographic unit cell because of the disordered displacement of the organic linkers with respect to the inorganic bricks. For the defect-containing samples, a reduced mechanical stability is observed, however, critically depending on the distribution of these defects throughout the material, hence demonstrating the importance of judiciously characterizing defects in these materials.

Bias-induced conductance switching in single molecule junctions containing a redox-active transition metal complex

ABSTRACT

The paper provides a comprehensive theoretical description of electron transport through transition metal complexes in single molecule junctions, where the main focus is on an analysis of the structural parameters responsible for bias-induced conductance switching as found in recent experiments, where an interpretation was provided by our simulations. The switching could be theoretically explained by a two-channel model combining coherent electron transport and electron hopping, where the underlying mechanism could be identified as a charging of the molecule in the junction made possible by the presence of a localized electronic state on the transition metal center. In this article, we present a framework for the description of an electron hopping-based switching process within the semi-classical Marcus-Hush theory, where all relevant quantities are calculated on the basis of density functional theory (DFT). Additionally, structural aspects of the junction and their respective importance for the occurrence of irreversible switching are discussed.

GRAPHICAL ABSTRACT

Involving High School Students in Computational Physics University Research: Theory Calculations of Toluene Adsorbed on Graphene

To increase public awareness of theoretical materials physics, a small group of high school students is invited to participate actively in a current research projects at Chalmers University of Technology. The Chalmers research group explores methods for filtrating hazardous and otherwise unwanted molecules from drinking water, for example by adsorption in active carbon filters. In this project, the students use graphene as an idealized model for active carbon, and estimate the energy of adsorption of the methylbenzene toluene on graphene with the help of the atomic-scale calculational method density functional theory. In this process the students develop an insight into applied quantum physics, a topic usually not taught at this educational level, and gain some experience with a couple of state-of-the-art calculational tools in materials research.