Showing papers by "Bjørk Hammer published in 2017"

The Atomic Simulation Environment - A Python library for working with atoms

Abstract: 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 simula- tions. 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.

Combining Evolutionary Algorithms with Clustering toward Rational Global Structure Optimization at the Atomic Scale.

Abstract: Predicting structures at the atomic scale is of great importance for understanding the properties of materials. Such predictions are infeasible without efficient global optimization techniques. Many current techniques produce a large amount of idle intermediate data before converging to the global minimum. If this information could be analyzed during optimization, many new possibilities emerge for more rational search algorithms. We combine an evolutionary algorithm (EA) and clustering, a machine-learning technique, to produce a rational algorithm for global structure optimization. Clustering the configuration space of intermediate structures into regions of geometrically similar structures enables the EA to suppress certain regions and favor others. For two test systems, an organic molecule and an oxide surface, the global minimum search proves significantly faster when favoring stable structures in unexplored regions. This clustering-enhanced EA is a step toward adaptive global optimization techniques t...

Substrate-induced semiconductor-to-metal transition in monolayer WS 2

Abstract: Low-resistance Ohmic contacts are a challenge for electronic devices based on two-dimensional (2D) materials. We show that an atomically precise in-plane junction between a 2D semiconductor and a metallic contact can lead to a semiconductor-to-metal transition in the 2D material, a finding which points the way to a possible method of achieving low-resistance junctions. Specifically, monolayer ${\mathrm{WS}}_{2}$ undergoes a semiconductor-to-metal transition when epitaxially grown with a high-quality interface on clean Ag(111), while it remains a semiconductor on Au(111). The metallicity of the single layer on Ag(111) is established by line-shape analysis of core-level photoemission spectra. Angle-resolved photoemission spectroscopy locates the metallic states near the $Q$ point of the ${\mathrm{WS}}_{2}$ Brillouin zone. Density functional theory calculations show that the metallic states arise from hybridization between Ag bulk bands and the local conduction-band minimum of ${\mathrm{WS}}_{2}$ near the $Q$ point.

Structure of the SnO2 (110)- (4×1) Surface

Abstract: Using surface x-ray diffraction (SXRD), quantitative low-energy electron diffraction (LEED), and density-functional theory (DFT) calculations, we have determined the structure of the ($4\ifmmode\times\else\texttimes\fi{}1$) reconstruction formed by sputtering and annealing of the ${\mathrm{SnO}}_{2}(110)$ surface. We find that the reconstruction consists of an ordered arrangement of ${\mathrm{Sn}}_{3}{\mathrm{O}}_{3}$ clusters bound atop the bulk-terminated ${\mathrm{SnO}}_{2}(110)$ surface. The model was found by application of a DFT-based evolutionary algorithm with surface compositions based on SXRD, and shows excellent agreement with LEED and with previously published scanning tunneling microscopy measurements. The model proposed previously consisting of in-plane oxygen vacancies is thus shown to be incorrect, and our result suggests instead that Sn(II) species in interstitial positions are the more relevant features of reduced ${\mathrm{SnO}}_{2}(110)$ surfaces.

Monitoring interconversion between stereochemical states in single chirality-transfer complexes on a platinum surface.

Abstract: Elementary steps in enantioselective heterogeneous catalysis take place on the catalyst surface and the targeted synthesis of a desired enantiomer requires the implantation of chiral information at the surface, which can be achieved-for example-by adsorbing chiral molecules. Studies of the structures of complexes formed between adsorbed prochiral reagents and chiral molecules yield information on the forces exerting stereocontrol, but further insight could be gained by studying the dynamics of their interactions. Here, using time-lapsed scanning tunnelling microscopy and density functional theory, we observe coupling between multiple stereochemical states within individual non-covalently bonded chirality-transfer complexes on a metal surface. We identify two modes of transformation between stereochemical states and find that the prochiral reagent can sample several complexation geometries during the lifetime of a complex, switching between states of opposing prochirality in the process. These results provide insight on the contribution of individual stereochemical states to the overall enantioselectivity of reactions occurring on catalyst surfaces.

Structure and Dynamics of Individual Diastereomeric Complexes on Platinum: Surface Studies Related to Heterogeneous Enantioselective Catalysis.

Abstract: ConspectusThe modification of heterogeneous catalysts through the chemisorption of chiral molecules is a method to create catalytic sites for enantioselective surface reactions. The chiral molecule is called a chiral modifier by analogy to the terms chiral auxiliary or chiral ligand used in homogeneous asymmetric catalysis. While there has been progress in understanding how chirality transfer occurs, the intrinsic difficulties in determining enantioselective reaction mechanisms are compounded by the multisite nature of heterogeneous catalysts and by the challenges facing stereospecific surface analysis. However, molecular descriptions have now emerged that are sufficiently detailed to herald rapid advances in the area. The driving force for the development of heterogeneous enantioselective catalysts stems, at the minimum, from the practical advantages they might offer over their homogeneous counterparts in terms of process scalability and catalyst reusability. The broader rewards from their study lie in t...

Water Gas Shift over Metal-Free Nanocrystalline Ceria: An Experimental and Theoretical Study

Abstract: A tandem experimental and theoretical investigation of a mesoporous ceria catalyst reveals the properties of the metal oxide are conducive for activity typically ascribed to metals, suggesting reduced Ce3+ and oxygen vacancies are responsible for the inherent bi-functionality of CO oxidation and dissociation of water required for facilitating the production of H2. The degree of reduction of the ceria, specifically the (100) face, is found to significantly influence the binding of reagents, suggesting reduced surfaces harbor the necessary reactive sites. The metal-free catalysis of the reaction is significant for catalyst design considerations, and the suite of in situ analyses provides a comprehensive study of the dynamic nature of the high surface area catalyst system. This study postulates feasible improvements in catalytic activity may redirect the purpose of the water-gas shift reaction from CO purification to primary hydrogen production.

Supramolecular Corrals on Surfaces Resulting from Aromatic Interactions of Nonplanar Triazoles.

Abstract: 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 re...

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

Abstract: 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...

Structure of the SnO2(110)-(4 x 1) Surface

Abstract: Using surface x-ray diffraction (SXRD), quantitative low-energy electron diffraction (LEED), and density-functional theory (DFT) calculations, we have determined the structure of the (4 × 1) reconstruction formed by sputtering and annealing of the SnO2ð110Þ surface We find that the reconstruction consists of an ordered arrangement of Sn3O3 clusters bound atop the bulk-terminated SnO2ð110Þ surface The model was found by application of a DFT-based evolutionary algorithm with surface compositions based on SXRD, and shows excellent agreement with LEED and with previously published scanning tunneling microscopy measurements The model proposed previously consisting of inplane oxygen vacancies is thus shown to be incorrect, and our result suggests instead that Sn(II) species in interstitial positions are the more relevant features of reduced SnO2ð110Þ surfaces