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

Visualizing hydrogen-induced reshaping and edge activation in MoS2 and Co-promoted MoS2 catalyst clusters

Hydrodesulfurization catalysis ensures upgrading and purification of fossil fuels to comply with increasingly strict regulations on S emissions. The future shift toward more diverse and lower-quality crude oil supplies, high in S content, requires attention to improvements of the complex sulfided CoMo catalyst based on a fundamental understanding of its working principles. In this study, we use scanning tunneling microscopy to directly visualize and quantify how reducing conditions transforms both cluster shapes and edge terminations in MoS₂ and promoted CoMoS-type hydrodesulfurization catalysts. The reduced catalyst clusters are shown to be terminated with a fractional coverage of sulfur, representative of the catalyst in its active state. By adsorption of a proton-accepting molecular marker, we can furthermore directly evidence the presence of catalytically relevant S–H groups on the Co-promoted edge. The experimentally observed cluster structure is predicted by theory to be identical to the structure present under catalytic working conditions.

Rational design of a hydrodesulfurization catalyst relies on a fundamental understanding of its working principles. Here, the authors use scanning tunneling microscopy to directly visualize and quantify hydrogen-induced reshaping and edge activation in MoS₂ and Co-promoted MoS₂ catalyst clusters.

Implanting Germanium into Graphene

Incorporating heteroatoms into the graphene lattice may be used to tailor its electronic, mechanical and chemical properties, although directly observed substitutions have thus far been limited to incidental Si impurities and P, N and B dopants introduced using low-energy ion implantation. We present here the heaviest impurity to date, namely ⁷⁴Ge⁺ ions implanted into monolayer graphene. Although sample contamination remains an issue, atomic resolution scanning transmission electron microscopy imaging and quantitative image simulations show that Ge can either directly substitute single atoms, bonding to three carbon neighbors in a buckled out-of-plane configuration, or occupy an in-plane position in a divacancy. First-principles molecular dynamics provides further atomistic insight into the implantation process, revealing a strong chemical effect that enables implantation below the graphene displacement threshold energy. Our results demonstrate that heavy atoms can be implanted into the graphene lattice, pointing a way toward advanced applications such as single-atom catalysis with graphene as the template.

Atomic Layer Deposition of Zinc Oxide: Study on the Water Pulse Reactions from First-Principles

Atomic layer deposition (ALD) of zinc oxide thin films has been under intense research in the past few years. The most common precursors used in this process are diethyl zinc (DEZ) and water. The surface chemistry related to the growth of a zinc oxide thin film via atomic layer deposition is not entirely clear, and the ideal model of the process has been contradicted by experimental data, e.g., the incomplete elimination of the ethyl ligands from the surface and the non-negative mass change during the water pulse. In this work we investigate the surface reactions of water during the atomic layer deposition of zinc oxide. The adsorption and ligand-exchange reactions of water are studied on ethyl-saturated surface structures to grasp the relevant surface chemistry contributing to the deposition process. The complex ethyl-saturated surface structures are adopted from a previous publication on the DEZ/H2O-process, and different configurations are sampled using ab initio molecular dynamics in order to find a suitable minimum structure. Water molecules are found to adsorb exothermically onto the ethyl-covered surface at all the ethyl concentrations considered. We do not observe an adsorption barrier for water at 0 K; however, the adsorption energy for any additional water molecules decreases rapidly at high ethyl concentrations. Ligand-exchange reactions are studied at various surface ethyl coverages. The water pulse ligand-exchange reactions have overall larger activation energies than surface reactions for diethyl zinc pulse. For some of the configurations considered, the reaction barriers may be inaccessible at the process conditions, suggesting that some ligands may be inert toward ligand-exchange with water. The activation energies for the surface reactions show only a weak dependence on the surface ethyl concentration. The sensitivity of the adsorption of water at high ethyl coverages suggests that at high ligand-coverages the kinetics may be somewhat hindered due to steric effects. Calculations on the ethyl-covered surfaces are compared to a simple model containing a single monoethyl zinc group. The calculated activation energy for this model is in line with calculations done on the complex model, but the adsorption of water is poorly described. The weak adsorption bond onto a single monoethyl zinc is probably due to a cooperative effect between the surface zinc atoms. A cooperative effect between water molecules is also observed; however, the effect on the activation energies is not as significant as has been reported for other ALD processes.

DFT Prediction of Enhanced Reducibility of Monoclinic Zirconia upon Rhodium Deposition

Oxides are an important class of materials and are widely used, for example, as supports in heterogeneous catalysis. In a number of industrial catalytic processes, oxide supports actively participate in chemical transformations by releasing lattice oxygen anions. While this is intuitively understood for reducible oxides, the reducibility of irreducible oxides may be modified via nanoengineering or upon inclusion of foreign species. Our calculations predict that the ability of irreducible monoclinic zirconia to release oxygen improves substantially upon deposition of rhodium. Through a comprehensive screening of Rh/ZrO₂ with different size of the rhodium species, we find that a Rh adatom and a Rh₄ nanocluster have the largest impact on the reducibility of zirconia. With increasing size the effect of rhodium decays. Our findings demonstrate that the phenomenon of enhanced reducibility of irreducible oxides in the presence of metals should be considered when interpreting experimental and computational results, as reactions that involve release of oxygen from an oxide support might be possible for irreducible oxides.

Rotation and diffusion of naphthalene on Pt(111)

The behavior of naphthalene on Pt(111) surfaces is studied by combining insight from scanning tunneling microscopy (STM) and van der Waals enabled density functional theory. Adsorption, diffusion, and rotation are investigated by a series of variable temperature STM experiments revealing naphthalene ability to rotate on-site with ease with a rotational barrier of 0.69 eV. Diffusion to neighbouring sites is found to be more difficult. The experimental results are in good agreement with the theoretical investigations which confirm that the barrier for diffusion is slightly higher than the one for rotation. The theoretical barriers for rotation and translation are found to be 0.75 and 0.78 eV, respectively. An automatic mapping of the possible diffusion pathways reveals very detailed diffusion paths with many small local minima that would have been practically impossible to find manually. This automated procedure provides detailed insight into the preferred diffusion pathways that are important for our understanding of molecule-substrate interactions.

NH3 adsorption on anatase-TiO2(101)

The adsorption of ammonia on anatase TiO₂ is of fundamental importance for several catalytic applications of TiO₂ and for probing acid-base interactions. Utilizing high-resolution scanning tunneling microscopy (STM), synchrotron X-ray photoelectron spectroscopy, temperature-programmed desorption (TPD), and density functional theory (DFT), we identify the adsorption mode and quantify the adsorption strength on the anatase TiO₂(101) surface. It was found that ammonia adsorbs non-dissociatively as NH₃ on regular five-fold coordinated titanium surface sites (5f-Ti) with an estimated exothermic adsorption energy of 1.2 eV for an isolated ammonia molecule. For higher adsorbate coverages, the adsorption energy progressively shifts to smaller values, due to repulsive intermolecular interactions. The repulsive adsorbate-adsorbate interactions are quantified using DFT and autocorrelation analysis of STM images, which both showed a repulsive energy of ∼50 meV for nearest neighbor sites and a lowering in binding energy for an ammonia molecule in a full monolayer of 0.28 eV, which is in agreement with TPD spectra.

Fullerene-Functionalized Monolayer-Protected Silver Clusters: [Ag29(BDT)12(C60) n]3- ( n = 1-9)

We report the formation of supramolecular adducts between monolayer-protected noble metal nanoclusters and fullerenes, specifically focusing on a well-known silver cluster, [Ag₂₉(BDT)₁₂]^3-, where BDT is 1,3-benzenedithiol. We demonstrate that C₆₀ molecules link with the cluster at specific locations and protect the fragile cluster core, enhancing the stability of the cluster. A combination of studies including UV-vis, high-resolution electrospray ionization mass spectrometry, collision-induced dissociation, and nuclear magnetic resonance spectroscopy revealed structural details of the fullerene-functionalized clusters, [Ag₂₉(BDT)₁₂(C₆₀) _n]^3- ( n = 1-9). Density functional theory (DFT) calculations and molecular docking simulations affirm compatibility between the cluster and C₆₀, resulting in its attachment at specific positions on the surface of the cluster, stabilized mainly by π-π and van der Waals interactions. The structures have also been confirmed from ion mobility mass spectrometry by comparing the experimental collision cross sections (CCSs) with the theoretical CCSs of the DFT-optimized structures. The gradual evolution of the structures with an increase in the number of fullerene attachments to the cluster has been investigated. Whereas the structure for n = 4 is tetrahedral, that of n = 8 is a distorted cube with a cluster at the center and fullerenes at the vertices. Another fullerene, C₇₀, also exhibited similar behavior. Modified clusters are expected to show interesting properties.

Anisotropy enhanced X-ray scattering from solvated transition metal complexes

Time-resolved X-ray scattering patterns from photoexcited molecules in solution are in many cases anisotropic at the ultrafast time scales accessible at X-ray free-electron lasers (XFELs). This anisotropy arises from the interaction of a linearly polarized UV-Vis pump laser pulse with the sample, which induces anisotropic structural changes that can be captured by femtosecond X-ray pulses. In this work, a method for quantitative analysis of the anisotropic scattering signal arising from an ensemble of molecules is described, and it is demonstrated how its use can enhance the structural sensitivity of the time-resolved X-ray scattering experiment. This method is applied on time-resolved X-ray scattering patterns measured upon photoexcitation of a solvated di-platinum complex at an XFEL, and the key parameters involved are explored. It is shown that a combined analysis of the anisotropic and isotropic difference scattering signals in this experiment allows a more precise determination of the main photoinduced structural change in the solute, i.e. the change in Pt-Pt bond length, and yields more information on the excitation channels than the analysis of the isotropic scattering only. Finally, it is discussed how the anisotropic transient response of the solvent can enable the determination of key experimental parameters such as the instrument response function.

Cyanographone and isocyanographone - Two asymmetrically functionalized graphene pseudohalides and their potential use in chemical sensing

Graphene pseudohalides are natural candidates for use in molecular sensing due to their greater chemical activity as compared to both graphene halides and pristine graphene. Though their study is still in its infancy, being hindered until recently by the unavailability of both selective and efficient procedures for their synthesis, they promise to considerably widen the application potential of chemically modified graphenes. Herein, we employ van der Waals density functional theory to study the structural and electronic properties of two selected graphene pseudohalides, namely, cyanographone and isocyanographone and investigate the potential use of the latter as a chemical sensor via electron transport calculations.

Local Plasmon Engineering in Doped Graphene

Single-atom B or N substitutional doping in single-layer suspended graphene, realized by low-energy ion implantation, is shown to induce a dampening or enhancement of the characteristic interband π plasmon of graphene through a high-resolution electron energy loss spectroscopy study using scanning transmission electron microscopy. A relative 16% decrease or 20% increase in the π plasmon quality factor is attributed to the presence of a single substitutional B or N atom dopant, respectively. This modification is in both cases shown to be relatively localized, with data suggesting the plasmonic response tailoring can no longer be detected within experimental uncertainties beyond a distance of approximately 1 nm from the dopant. Ab initio calculations confirm the trends observed experimentally. Our results directly confirm the possibility of tailoring the plasmonic properties of graphene in the ultraviolet waveband at the atomic scale, a crucial step in the quest for utilizing graphene's properties toward the development of plasmonic and optoelectronic devices operating at ultraviolet frequencies.

Revealing the Chemistry between Band Gap and Binding Energy for Lead-/Tin-Based Trihalide Perovskite Solar Cell Semiconductors

A relationship between reported experimental band gaps (solid) and DFT-calculated binding energies (gas) is established, for the first time, for each of the four ten-membered lead (or tin) trihalide perovskite solar cell semiconductor series examined in this study, including CH₃ NH₃ PbY₃ , CsPbY₃ , CH₃ NH₃ SnY₃ and CsSnY₃ (Y=I_(3-x) Br_x=1-3 , I_(3-x) Cl_x=1-3 , Br_(3-x) Cl _x=1-3 , and IBrCl). The relationship unequivocally provides a new dimension for the fundamental understanding of the optoelectronic features of solid-state solar cell thin films by using the 0 K gas-phase energetics of the corresponding molecular building blocks.

Exciting H2 Molecules for Graphene Functionalization

Hydrogen functionalization of graphene by exposure to vibrationally excited H₂ molecules is investigated by combined scanning tunneling microscopy, high-resolution electron energy loss spectroscopy, X-ray photoelectron spectroscopy measurements, and density functional theory calculations. The measurements reveal that vibrationally excited H₂ molecules dissociatively adsorb on graphene on Ir(111) resulting in nanopatterned hydrogen functionalization structures. Calculations demonstrate that the presence of the Ir surface below the graphene lowers the H₂ dissociative adsorption barrier and allows for the adsorption reaction at energies well below the dissociation threshold of the H-H bond. The first reacting H₂ molecule must contain considerable vibrational energy to overcome the dissociative adsorption barrier. However, this initial adsorption further activates the surface resulting in reduced barriers for dissociative adsorption of subsequent H₂ molecules. This enables functionalization by H₂ molecules with lower vibrational energy, yielding an avalanche effect for the hydrogenation reaction. These results provide an example of a catalytically active graphene-coated surface and additionally set the stage for a re-interpretation of previous experimental work involving elevated H₂ background gas pressures in the presence of hot filaments.

Dynamic Stabilization of the Ligand-Metal Interface in Atomically Precise Gold Nanoclusters Au68 and Au144 Protected by meta-Mercaptobenzoic Acid

Ligand-stabilized, atomically precise gold nanoclusters with a metal core of a uniform size of just 1-3 nm constitute an interesting class of nanomaterials with versatile possibilities for applications due to their size-dependent properties and modifiable ligand layers. The key to extending the usability of the clusters in applications is to understand the chemical bonding in the ligand layer as a function of cluster size and ligand structure. Previously, it has been shown that monodispersed gold nanoclusters, stabilized by meta-mercaptobenzoic acid (m-MBA or 3-MBA) ligands and with sizes of 68-144 gold atoms, show ambient stability. Here we show that a combination of nuclear magnetic resonance spectroscopy, UV-vis absorption, infrared spectroscopy, molecular dynamics simulations, and density functional theory calculations reveals a distinct chemistry in the ligand layer, absent in other known thiol-stabilized gold nanoclusters. Our results imply a low-symmetry C₁ ligand layer of 3-MBA around the gold core of Au₆₈ and Au₁₄₄ and suggest that 3-MBA protects the metal core not only by the covalent S-Au bond formation but also via weak π-Au and O═C-OH···Au interactions. The π-Au and -OH···Au interactions have a strength of the order of a hydrogen bond and thus are dynamic in water at ambient temperature. The -OH···Au interaction was identified by a distinct carbonyl stretch frequency that is distinct for 3-MBA-protected gold clusters, but is missing in the previously studied Au₁₀₂(p-MBA)₄₄ cluster. These thiol-gold interactions can be used to explain a remarkably low ligand density on the surface of the metal core of these clusters. Our results lay a foundation to understand functionalization of atomically precise ligand-stabilized gold nanoclusters via a route where weak ligand-metal interfacial interactions are sacrificed for covalent bonding.

Patterning of supported gold monolayers via chemical lift-off lithography

The supported monolayer of Au that accompanies alkanethiolate molecules removed by polymer stamps during chemical lift-off lithography is a scarcely studied hybrid material. We show that these Au-alkanethiolate layers on poly(dimethylsiloxane) (PDMS) are transparent, functional, hybrid interfaces that can be patterned over nanometer, micrometer, and millimeter length scales. Unlike other ultrathin Au films and nanoparticles, lifted-off Au-alkanethiolate thin films lack a measurable optical signature. We therefore devised fabrication, characterization, and simulation strategies by which to interrogate the nanoscale structure, chemical functionality, stoichiometry, and spectral signature of the supported Au-thiolate layers. The patterning of these layers laterally encodes their functionality, as demonstrated by a fluorescence-based approach that relies on dye-labeled complementary DNA hybridization. Supported thin Au films can be patterned via features on PDMS stamps (controlled contact), using patterned Au substrates prior to lift-off (e.g., selective wet etching), or by patterning alkanethiols on Au substrates to be reactive in selected regions but not others (controlled reactivity). In all cases, the regions containing Au-alkanethiolate layers have a sub-nanometer apparent height, which was found to be consistent with molecular dynamics simulations that predicted the removal of no more than 1.5 Au atoms per thiol, thus presenting a monolayer-like structure.

Reversible Anion-Driven Switching of an Organic 2D Crystal at a Solid-Liquid Interface

Ionic self-assembly of charged molecular building blocks relies on the interplay between long-range electrostatic forces and short-range, often cooperative, supramolecular interactions, yet has been seldom studied in two dimensions at the solid-liquid interface. Here, we demonstrate anion-driven switching of two-dimensional (2D) crystal structure at the Au(111)/octanoic acid interface. Using scanning tunneling microscopy (STM), three organic salts with identical polyaromatic cation (PQPC₆⁺ ) but different anions (perchlorate, anthraquinonedisulfonate, benzenesulfonate) are shown to form distinct, highly ordered self-assembled structures. Reversible switching of the supramolecular arrangement is demonstrated by in situ exchange of the anion on the pre-formed adlayer, by changing the concentration ratio between the incoming and outgoing anion. Density functional theory (DFT) calculations reveal that perchlorate is highly mobile in the adlayer, and corroborate why this anion is only resolved transiently in STM. Surprisingly, the templating effect of the anion persists even where it does not become part of the adlayer 2D fabric, which we ascribe to differences in stabilization of cation conformations by the anion. Our results provide important insight into the structuring of mixed anion-cation adlayers. This is essential in the design of tectons for ionic self-assembled superstructures and biomimetic adaptive materials and valuable also to understand adsorbate-adsorbate interactions in heterogeneous catalysis.

A Simply Synthesized, Tough Polyarylene with Transient Mechanochromic Response

A simple and high-yielding route to tough polyarylenes of the type poly(meta,meta,para-phenylene) (PmmpP) is developed. PmmpP is tough even in its as-synthesized state which has an intermediate molar mass of M_w ≈60 kg mol^-1 and exhibits outstanding mechanical properties at further optimized molecular weight of M_w =96 kg mol^-1 , E=0.9 GPa, ϵ=300 %. Statistical copolymers with para,para-spiropyran (SP) are mechanochromic, and the toughness allows mechanochromism to be investigated. Strained samples instantaneously lose color upon force release. DFT calculations show this phenomenon to be caused by the PmmpP matrix that allows build-up of sufficiently large forces to be transduced to SP, and the relatively unstable corresponding merocyanine (MC) form arising from the aromatic co-monomer. MC units covalently incorporated into PmmpP show a drastically reduced half life time of 3.1 s compared to 4.5 h obtained for SP derivatives with common 6-nitro substitution.

Methane Adsorption in Zr-Based MOFs: Comparison and Critical Evaluation of Force Fields

The search for nanoporous materials that are highly performing for gas storage and separation is one of the contemporary challenges in material design. The computational tools to aid these experimental efforts are widely available, and adsorption isotherms are routinely computed for huge sets of (hypothetical) frameworks. Clearly the computational results depend on the interactions between the adsorbed species and the adsorbent, which are commonly described using force fields. In this paper, an extensive comparison and in-depth investigation of several force fields from literature is reported for the case of methane adsorption in the Zr-based Metal-Organic Frameworks UiO-66, UiO-67, DUT-52, NU-1000, and MOF-808. Significant quantitative differences in the computed uptake are observed when comparing different force fields, but most qualitative features are common which suggests some predictive power of the simulations when it comes to these properties. More insight into the host-guest interactions is obtained by benchmarking the force fields with an extensive number of ab initio computed single molecule interaction energies. This analysis at the molecular level reveals that especially ab initio derived force fields perform well in reproducing the ab initio interaction energies. Finally, the high sensitivity of uptake predictions on the underlying potential energy surface is explored.

Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex

A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H₂O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt₂(P₂O₅H₂)₄]^4- complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.

Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block

The DNA double helix is a versatile building block used in DNA nanotechnology. To potentiate the discovery of new DNA nanoscale assemblies, recently, silver cations have been introduced to pair DNA strands by base-Ag⁺-base bonding rather than by Watson-Crick pairing. In this work, we study the classical dynamics of a parallel silver-mediated homobase double helix and compare it to the dynamics of the antiparallel double helix. Our classical simulations show that only the parallel double helix is highly stable through the 100 ns simulation time. A new type of H-bond previously proposed by our collaboration and recently observed in crystal-determined helices drives the physicochemical stabilization. Compared to the natural B-DNA form, the metal-mediated helix has a contracted axial base pair rise and smaller numbers of base pairs per turn. These results open the path for the inclusion of this robust metal-mediated building block into new nanoscale DNA assemblies.

Influence of CH···N Interaction in the Self-Assembly of an Oligo(isoquinolyne-ethynylyne) Molecule with Distinct Conformational States

Molecular conformational flexibility can play an important role in supramolecular self-assembly on surfaces, affecting not least chiral molecular assemblies. To explicitly and systematically investigate the role of molecular conformational flexibility in surface self-assembly, we synthesized a three-bit conformational switch where each of three switching units on the molecules can assume one of two distinct binary positions on the surface. The molecules are designed to promote C-H···N type hydrogen bonds between the switching units. While supramolecular self-assembly based on strong hydrogen-bonding interactions has been widely explored, less is known about the role of such weaker directional interactions for surface self-assembly. The synthesized molecules consist of three nitrogen-containing isoquinoline (IQ) bits connected by ethynylene spokes and terminated by tert-butyl (tBu) groups. Using high-resolution scanning tunnelling microscopy, we investigate the self-assembly of the IQ-tBu molecules on a Au(111) surface under ultrahigh-vacuum conditions. The molecules form extended domains of brick-wall structure where the molecular backbones are packed regularly but without selection of specific molecular conformations. However, statistical analysis of the extended network demonstrates alignment/correlation for the orientations of the switching units indicating specific interactions. The primary interaction motifs in the structure are quantified from DFT calculations, showing that the brick-wall structure is indeed stabilized by two types of weak C-H···N bonds, involving either aromatic hydrogens on the IQ groups or nonaromatic hydrogens on the tBu groups. Analysis of the C-H···N interactions in the brick-wall structure explains the observed distribution and alignment of molecular conformations as well as the overall organization of the molecular surface structures.

Understanding activity and selectivity of metal-nitrogen-doped carbon catalysts for electrochemical reduction of CO2

Direct electrochemical reduction of CO₂ to fuels and chemicals using renewable electricity has attracted significant attention partly due to the fundamental challenges related to reactivity and selectivity, and partly due to its importance for industrial CO₂-consuming gas diffusion cathodes. Here, we present advances in the understanding of trends in the CO₂ to CO electrocatalysis of metal- and nitrogen-doped porous carbons containing catalytically active M–N_x moieties (M = Mn, Fe, Co, Ni, Cu). We investigate their intrinsic catalytic reactivity, CO turnover frequencies, CO faradaic efficiencies and demonstrate that Fe–N–C and especially Ni–N–C catalysts rival Au- and Ag-based catalysts. We model the catalytically active M–N_x moieties using density functional theory and correlate the theoretical binding energies with the experiments to give reactivity-selectivity descriptors. This gives an atomic-scale mechanistic understanding of potential-dependent CO and hydrocarbon selectivity from the M–N_x moieties and it provides predictive guidelines for the rational design of selective carbon-based CO₂ reduction catalysts.

Inexpensive and selective electrocatalysts for CO₂ reduction hold promise for sustainable fuel production. Here, the authors report N-coordinated, non-noble metal-doped porous carbons as efficient and selective electrocatalysts for CO₂ to CO conversion.

Electronic structure, transport, and collective effects in molecular layered systems

The great potential of organic heterostructures for organic device applications is exemplified by the targeted engineering of the electronic properties of phthalocyanine-based systems. The transport properties of two different phthalocyanine systems, a pure copper phthalocyanine (CoPc) and a flourinated copper phthalocyanine-manganese phthalocyanine (F16CoPc/MnPc) heterostructure, are investigated by means of density functional theory (DFT) and the non-equilibrium Green's function (NEGF) approach. Furthermore, a master-equation-based approach is used to include electronic correlations beyond the mean-field-type approximation of DFT. We describe the essential theoretical tools to obtain the parameters needed for the master equation from DFT results. Finally, an interacting molecular monolayer is considered within a master-equation approach.

Atomic Scale Formation Mechanism of Edge Dislocation Relieving Lattice Strain in a GeSi overlayer on Si(001)

Understanding how edge misfit dislocations (MDs) form in a GeSi/Si(001) film has been a long standing issue. The challenge is to find a mechanism accounting for the presence of these dislocations at the interface since they are not mobile and cannot nucleate at the surface and glide towards the interface. Furthermore, experiments can hardly detect the nucleation and early stages of growth because of the short time scale involved. Here we present the first semi-quantitative atomistic calculation of the formation of edge dislocations in such films. We use a global optimization method and density functional theory calculations, combined with computations using potential energy functions to identify the best mechanisms. We show that those previously suggested are relevant only for a low film strain and we propose a new mechanism which accounts for the formation of edge dislocations at high film strain. In this one, a 60° MD nucleates as a “split” half-loop with two branches gliding on different planes. One branch belongs to the glide plane of a complementary 60° MD and therefore strongly favors the formation of the complementary MD which is immediately combined with the first MD to form an edge MD.

Layered van der Waals crystals with hyperbolic light dispersion

Compared to artificially structured hyperbolic metamaterials, whose performance is limited by the finite size of the metallic components, the sparse number of naturally hyperbolic materials recently discovered are promising candidates for the next generation of hyperbolic materials. Using first-principles calculations, we extend the number of known naturally hyperbolic materials to the broad class of layered transition metal dichalcogenides (TMDs). The diverse electronic properties of the transition metal dichalcogenides result in a large variation of the hyperbolic frequency regimes ranging from the near-infrared to the ultraviolet. Combined with the emerging field of van der Waals heterostructuring, we demonstrate how the hyperbolic properties can be further controlled by stacking different two-dimensional crystals opening new perspectives for atomic-scale design of photonic metamaterials. As an application, we identify candidates for Purcell factor control of emission from diamond nitrogen-vacancy centers.

Natural hyperbolic materials retain the peculiar optical properties of traditional metamaterials whilst not requiring artificial structuring. Here, the authors perform a theoretical screening of a large class of natural materials with hyperbolic dispersion among the family of layered transition metal dichalcogenides.

Supramolecular Corrals on Surfaces Resulting from Aromatic Interactions of Nonplanar Triazoles

Interaction forces between aromatic moieties, often referred to as π-π interactions, are an important element in stabilizing complex supramolecular structures. For supramolecular self-assembly occurring on surfaces, where aromatic moieties are typically forced to adsorb coplanar with the surface, the possible role of intermolecular aromatic interactions is much less explored. Here, we report on unusual, ring-shaped supramolecular corral surface structures resulting from adsorption of a molecule with nonplanar structure, allowing for intermolecular aromatic interactions. The discrete corral structures are observed using high-resolution scanning tunneling microscopy, and the energetic driving forces for their formation are elucidated using density functional theory calculations and Monte Carlo simulations. The individual corrals involve between 11 and 18 molecules bound through triazole moieties to a ring-shaped ensemble of bridge site positions on (111) surfaces of copper, silver, or gold. The curvature required to form the corrals is identified to result from the angle dependence of aromatic interactions between molecular phenanthrene moieties. The study provides detailed quantitative insights into triazole-surface and aromatic interactions and illustrates how they may be used to drive surface supramolecular self-assembly.

Visualizing atomic-scale redox dynamics in vanadium oxide-based catalysts

Surface redox processes involving oxygen atom exchange are fundamental in catalytic reactions mediated by metal oxides. These processes are often difficult to uncover due to changes in the surface stoichiometry and atomic arrangement. Here we employ high-resolution transmission electron microscopy to study vanadium oxide supported on titanium dioxide, which is of relevance as a catalyst in, e.g., nitrogen oxide emission abatement for environmental protection. The observations reveal a reversible transformation of the vanadium oxide surface between an ordered and disordered state, concomitant with a reversible change in the vanadium oxidation state, when alternating between oxidizing and reducing conditions. The transformation depends on the anatase titanium dioxide surface termination and the vanadium oxide layer thickness, suggesting that the properties of vanadium oxide are sensitive to the supporting oxide. These atomic-resolution observations offer a basis for rationalizing previous reports on shape-sensitive catalytic properties.

Redox processes in metal oxide surfaces can exhibit structure sensitivities which are difficult to uncover. Here, the authors use atomic-resolution imaging to demonstrate facet dependent alterations in the surfaces of supported vanadium oxide upon reduction and oxidation.

Real-Time Elucidation of Catalytic Pathways in CO Hydrogenation on Ru

The direct elucidation of the reaction pathways in heterogeneous catalysis has been challenging due to the short-lived nature of reaction intermediates. Here, we directly measured on ultrafast time scales the initial hydrogenation steps of adsorbed CO on a Ru catalyst surface, which is known as the bottleneck reaction in syngas and CO₂ reforming processes. We initiated the hydrogenation of CO with an ultrafast laser temperature jump and probed transient changes in the electronic structure using real-time X-ray spectroscopy. In combination with theoretical simulations, we verified the formation of CHO during CO hydrogenation.

Excitation-dependent fluorescence from atomic/molecular layer deposited sodium-uracil thin films

Atomic/molecular layer deposition (ALD/MLD) offers unique possibilities in the fabrication of inorganic-organic thin films with novel functionalities. Especially, incorporating nucleobases in the thin-film structures could open new avenues in the development of bio-electronic and photonic devices. Here we report an intense blue and widely excitation-dependent fluorescence in the visible region for ALD/MLD fabricated sodium-uracil thin films, where the crystalline network is formed from hydrogen-bonded uracil molecules linked via Na atoms. The excitation-dependent fluorescence is caused by the red-edge excitation shift (REES) effect taking place in the red-edge of the absorption spectrum, where the spectral relaxation occurs in continuous manner as demonstrated by the time-resolved measurements.

The NEST Dry-Run Mode: Efficient Dynamic Analysis of Neuronal Network Simulation Code

NEST is a simulator for spiking neuronal networks that commits to a general purpose approach: It allows for high flexibility in the design of network models, and its applications range from small-scale simulations on laptops to brain-scale simulations on supercomputers. Hence, developers need to test their code for various use cases and ensure that changes to code do not impair scalability. However, running a full set of benchmarks on a supercomputer takes up precious compute-time resources and can entail long queuing times. Here, we present the NEST dry-run mode, which enables comprehensive dynamic code analysis without requiring access to high-performance computing facilities. A dry-run simulation is carried out by a single process, which performs all simulation steps except communication as if it was part of a parallel environment with many processes. We show that measurements of memory usage and runtime of neuronal network simulations closely match the corresponding dry-run data. Furthermore, we demonstrate the successful application of the dry-run mode in the areas of profiling and performance modeling.

The atomic simulation environment-a Python library for working with atoms

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Computational insights and the observation of SiC nanograin assembly: towards 2D silicon carbide

While an increasing number of two-dimensional (2D) materials, including graphene and silicene, have already been realized, others have only been predicted. An interesting example is the two-dimensional form of silicon carbide (2D-SiC). Here, we present an observation of atomically thin and hexagonally bonded nanosized grains of SiC assembling temporarily in graphene oxide pores during an atomic resolution scanning transmission electron microscopy experiment. Even though these small grains do not fully represent the bulk crystal, simulations indicate that their electronic structure already approaches that of 2D-SiC. This is predicted to be flat, but some doubts have remained regarding the preference of Si for sp³ hybridization. Exploring a number of corrugated morphologies, we find completely flat 2D-SiC to have the lowest energy. We further compute its phonon dispersion, with a Raman-active transverse optical mode, and estimate the core level binding energies. Finally, we study the chemical reactivity of 2D-SiC, suggesting it is like silicene unstable against molecular absorption or interlayer linking. Nonetheless, it can form stable van der Waals-bonded bilayers with either graphene or hexagonal boron nitride, promising to further enrich the family of two-dimensional materials once bulk synthesis is achieved.

Formation of Germa-ketenimine on the Ge(100) Surface by Adsorption of tert-Butyl Isocyanide

Reactions of the (100) surfaces of Ge and Si with organic molecules have been generally understood within the concept of "dimers" formed by the 2 × 1 surface reconstruction. In this work, the adsorption of tert-butyl isocyanide on the Ge(100)-2 × 1 surface at large exposures is investigated under ultrahigh vacuum conditions. A combination of infrared spectroscopy, X-ray photoelectron spectroscopy, and temperature-programmed desorption experiments along with dispersion-corrected density functional theory calculations is used to determine the surface products. Upon adsorption of a dense monolayer of tert-butyl isocyanide, a product whose structure resembles a germa-ketenimine (N=C=Ge) with σ donation toward and π back-donation from the Ge(100) surface appears. Formation of this structure involves divalent-type surface Ge atoms that arise from cleavage of the Ge(100)-2 × 1 surface dimers. Our results reveal an unprecedented class of reactions of organic molecules at the Ge(100) surface.

Manifestation of Geometric and Electronic Shell Structures of Metal Clusters in Intercluster Reactions

Monolayer protected clusters exhibit rich diversity in geometric and electronic structures. However, structure-reactivity relationships in these clusters are rarely explored. In this context, [Ag₄₄(SR)₃₀]^4-, where -SR is an alkyl/aryl thiolate, is an interesting system due to its geometrically and electronically closed-shell structures and distinct charge states. We demonstrate that these structural features of [Ag₄₄(SR)₃₀]^4- are distinctly manifested in its solution-state reaction with another cluster, [Au₂₅(SR)₁₈]^-. Through this reaction, an alloy cluster anion, [Au₁₂Ag₃₂(SR)₃₀]^4-, evolves spontaneously as revealed by high-resolution electrospray ionization mass spectrometry. Ultraviolet-visible absorption spectroscopy and density functional theory calculations indicate that [Au₁₂Ag₃₂(SR)₃₀]^4- is formed by the substitution of all of the Ag atoms in the innermost icosahedral shell of [Ag₄₄(SR)₃₀]^4- and the abundance is attributed to its higher stability due to closed geometric as well as electronic shell structure, similar to the reactant clusters. We further demonstrate that the substitution of metal atoms in the middle dodecahedral shell and the outermost mount sites are also possible, however such substitutions produce Au_xAg_44-x(SR)₃₀ alloy clusters with geometrically and electronically open shells. Depending on specific sites of substitution, an unexpected superatom-nonsuperatom transition occurs in the distribution of Au_xAg_44-x(SR)₃₀ alloy clusters formed in this reaction. Our results present a unique example of a structure-reactivity relationship in the metal atom substitution chemistry of monolayer protected clusters, wherein a systematic trend, reflecting the geometric and the electronic shell structures of the reactant as well as the product clusters, was observed.

Buckyball sandwiches

Two-dimensional (2D) materials have considerably expanded the field of materials science in the past decade. Even more recently, various 2D materials have been assembled into vertical van der Waals heterostacks, and it has been proposed to combine them with other low-dimensional structures to create new materials with hybridized properties. We demonstrate the first direct images of a suspended 0D/2D heterostructure that incorporates C₆₀ molecules between two graphene layers in a buckyball sandwich structure. We find clean and ordered C₆₀ islands with thicknesses down to one molecule, shielded by the graphene layers from the microscope vacuum and partially protected from radiation damage during scanning transmission electron microscopy imaging. The sandwich structure serves as a 2D nanoscale reaction chamber, allowing the analysis of the structure of the molecules and their dynamics at atomic resolution.

Single-molecule spin orientation control by an electric field

We report the effects of an electric field E on the spin orientations of nickelocene (Nc) deposited on the Cu surfaces by means of first-principles calculations. We employ the Hubbard-U corrected van der Waals density functional to take into account the strong correlation effects of the localized 3d electrons and the non-covalent binding involved in the molecule-surface coupling. We show that the deposited Nc molecule can switch between in-plane (in small E-field) and perpendicular magnetization (in large E-field). We find that the significant charge transfer between the molecule and the metallic surface plays a dominant role in the spin reorientation transition. From an electronic structure perspective, the shift in the Fermi level enhances the coupling between the occupied and unoccupied Ni-3d states of different spin states, which tends to facilitate the perpendicular magnetic anisotropy. These findings shed some light on the electrical control of the magnetic anisotropies of single-molecule magnets on metal surfaces.

Determination of Conduction and Valence Band Electronic Structure of LaTiOx Ny Thin Film

The nitrogen substitution into the oxygen sites of several oxide materials leads to a reduction of the band gap to the visible-light energy range, which makes these oxynitride semiconductors potential photocatalysts for efficient solar water splitting. Oxynitrides typically show a different crystal structure compared to the pristine oxide material. As the band gap is correlated to both the chemical composition and the crystal structure, it is not trivial to distinguish which modifications of the electronic structure induced by the nitrogen substitution are related to compositional and/or structural effects. Here, X-ray emission and absorption spectroscopy are used to investigate the electronic structures of orthorhombic perovskite LaTiO_x N_y thin films in comparison with films of the pristine oxide LaTiO_x with similar orthorhombic structure and cationic oxidation state. Experiment and theory show the expected upward shift in energy of the valence band maximum that reduces the band gap as a consequence of the nitrogen incorporation. This study also shows that the conduction band minimum, typically considered almost unaffected by nitrogen substitution, undergoes a significant downward shift in energy. For a rational design of oxynitride photocatalysts, the observed changes of both the unoccupied and occupied electronic states have to be taken into account to justify the total band-gap narrowing induced by the nitrogen incorporation.