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 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

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

Exciting H 2 molecules for graphene functionalization

20siHydrogen 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.reservedmixedKyhl, Line; Bisson, Régis; Balog, Richard; Groves, Michael N.; Kolsbjerg, Esben Leonhard; Cassidy, Andrew Martin; Jørgensen, Jakob Holm; Halkjær, Susanne; Miwa, Jill A.; Čabo, Antonija Grubišić; Angot, Thierry; Hofmann, Philip; Arman, Mohammad Alif; Urpelainen, Samuli; Lacovig, Paolo; Bignardi, Luca; Bluhm, Hendrik; Knudsen, Jan; Hammer, Bjørk; Hornekaer, LivKyhl, Line; Bisson, Régis; Balog, Richard; Groves, Michael N.; Kolsbjerg, Esben Leonhard; Cassidy, Andrew Martin; Jørgensen, Jakob Holm; Halkjær, Susanne; Miwa, Jill A.; Čabo, Antonija Grubišić; Angot, Thierry; Hofmann, Philip; Arman, Mohammad Alif; Urpelainen, Samuli; Lacovig, Paolo; Bignardi, Luca; Bluhm, Hendrik; Knudsen, Jan; Hammer, Bjørk; Hornekaer, Li

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

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