Marcella Iannuzzi

cp2k: atomistic simulations of condensed matter systems

cp2k has become a versatile open‐source tool for the simulation of complex systems on the nanometer scale. It allows for sampling and exploring potential energy surfaces that can be computed using a variety of empirical and first principles models. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern and massively parallel hardware. This review briefly summarizes the main capabilities and illustrates with recent applications the science cp2k has enabled in the field of atomistic simulation. WIREs Comput Mol Sci 2014, 4:15–25. doi: 10.1002/wcms.1159

Boron Nitride on Cu(111): An Electronically Corrugated Monolayer

Ultrathin films of boron nitride (BN) have recently attracted considerable interest given their successful incorporation in graphene nanodevices and their use as spacer layers to electronically decouple and order functional adsorbates. Here, we introduce a BN monolayer grown by chemical vapor deposition of borazine on a single crystal Cu support, representing a model system for an electronically patterned but topographically smooth substrate. Scanning tunneling microscopy and spectroscopy experiments evidence a weak bonding of the single BN sheet to Cu, preserving the insulating character of bulk hexagonal boron nitride, combined with a periodic lateral variation of the local work function and the surface potential. Complementary density functional theory calculations reveal a varying registry of the BN relative to the Cu lattice as origin of this electronic Moiré-like superstructure.

Hexagonal boron nitride on transition metal surfaces

We validate a computational setup based on density functional theory to investigate hexagonal boron nitride (h-BN) monolayers grown on different transition metals exposing hexagonal surfaces. An extended assessment of our approach for the characterization of the geometrical and electronic structure of such systems is performed. Due to the lattice mismatch with the substrate, the monolayers can form Moiré-type superstructures with very long periodicities on the surface. Thus, proper models of these interfaces require very large simulation cells (more than 1,000 atoms) and an accurate description of interactions that are modulated with the specific registry of h-BN on the metal. We demonstrate that efficient and accurate calculations can be performed in such large systems using Gaussian basis sets and dispersion corrections to the (semi-)local density functionals. Four different metallic substrates, Rh(111), Ru(0001), Cu(111), and Ni(111), are explicitly considered, and the results are compared with previous experimental and computational studies.

Nanotexture Switching of Single-Layer Hexagonal Boron Nitride on Rhodium by Intercalation of Hydrogen Atoms†

The interaction of atomic hydrogen with a single layer of hexagonal boron nitride on rhodium leads to a removal of the h-BN surface corrugation. The process is reversible as the hydrogen may be expelled by annealing to about 500 K whereupon the texture on the nanometer scale is restored. This effect is traced back to hydrogen intercalation. It is expected to have implications for applications, like the storage of hydrogen, the peeling of sp2-hybridized layers from solid substrates or the control of the wetting angle, to name a few.Playing nano-tectonics: The interaction of atomic hydrogen with a single layer of hexagonal boron nitride on rhodium leads to the removal of the h-BN surface corrugation (see picture; blue region: corrugated, orange region: flat). This change of surface texture arises from the intercalation of hydrogen atoms between the h-BN skin and the metal, and can be restored by annealing to about 600 K to expel the hydrogen atoms.

X-ray absorption spectra of hexagonal ice and liquid water by all-electron Gaussian and augmented plane wave calculations

Full potential x-ray spectroscopy simulations of hexagonal ice and liquid water are performed by means of the newly implemented methodology based on the Gaussian augmented plane waves formalism. The computed spectra obtained within the supercell approach are compared to experimental data. The variations of the spectral distribution determined by the quality of the basis set, the size of the sample, and the choice of the core-hole potential are extensively discussed. The second part of this work is focused on the understanding of the connections between specific configurations of the hydrogen bond network and the corresponding contributions to the x-ray absorption spectrum in liquid water. Our results confirm that asymmetrically coordinated molecules, in particular, those donating only one or no hydrogen bond, are associated with well identified spectral signatures that differ significantly from the ice spectral profile. However, transient local structures, with half formed hydrogen bonds, may still give rise to spectra with dominant postedge contributions and relatively weaker oscillator strengths at lower energy. This explains why by averaging the spectra over all the O atoms of liquid instantaneous configurations extracted from ab initio molecular dynamics trajectories, the spectral features indicating the presence of weak or broken hydrogen bonds turn out to be attenuated and sometimes not clearly distinguishable.

Ab Initio Molecular Dynamics Study of Water Oxidation Reaction Pathways in Mono-Ru Catalysts

Ab initio molecular dynamics simulations with an adaptive biasing potential are carried out to study the reaction path in mononuclear Ru catalysts for water oxidation of the type [(Ar)Ru(X)(bpy)](+) with different aromatic ligands (Ar). The critical step of the O-O bond formation in the catalytic cycle starting from the [(Ar)Ru(O)(bpy)](2+) intermediate is analyzed in detail. It is shown that an explicit inclusion of the solvent environment is essential for a realistic description of the reaction path. Clear evidence is presented for a concerted reaction in which the O-O bond formation is quickly followed by a proton transfer leading to a Ru-OOH intermediate and a hydronium ion. An alternative path in which the approaching water first coordinates to the metal centre is also investigated, and it is found to induce a structural instability of the catalyst with the breaking of the aromatic ligand coordination bond.

Simulation of Adsorption Processes at Metallic Interfaces: An Image Charge Augmented QM/MM Approach.

A novel method for including polarization effects within hybrid quantum mechanics/molecular mechanics (QM/MM) simulations of adsorbate-metal systems is presented. The interactions between adsorbate (QM) and metallic substrate (MM) are described at the MM level of theory. Induction effects are additionally accounted for by applying the image charge formulation. The charge distribution induced within the metallic substrate is modeled by a set of Gaussian charges (image charges) centered at the metal atoms. The image charges and the electrostatic response of the QM potential are determined self-consistently by imposing the constant-potential condition within the metal. The implementation is embedded in a highly efficient Gaussian and plane wave framework and is naturally suited for periodic systems. Even though the electronic properties of the metallic substrate are not taken into account explicitly, the augmented QM/MM scheme can reproduce characteristic polarization effects of the adsorbate. The method is assessed through the investigation of structural and electronic properties of benzene, nitrobenzene, thymine, and guanine on Au(111). The study of small water clusters adsorbed on Pt(111) is also reported in order to demonstrate that the approach provides a sizable correction of the MM-based interactions between adsorbate and substrate. Large-scale molecular dynamics (MD) simulations of a water film in contact with a Pt(111) surface show that the method is suitable for simulations of liquid/metal interfaces at reduced computational cost.

Adsorption of Naphthalene and Quinoline on Pt, Pd and Rh: A DFT Study

The adsorption of naphthalene and quinoline on Pt(111), Pd(111) and Rh(111) surfaces is studied using density functional theory. The metal surfaces are simulated by means of large confined clusters and for Pt by means of a slab with periodic boundary conditions (PBC). Calculation parameters such as basis set convergence, basis set superposition error and effects of cluster relaxation and size are analyzed in order to assess the aptness of the cluster model. For all the metals, the preferred sites of adsorption are analyzed, thus revealing their different behaviors concerning structure and stability of adsorption modes. On Pt, the molecules have the richest theoretical configurational variety. Naphthalene and quinoline are found to adsorb preferentially on di-bridge[7] sites on the three metals, and Rh exhibits higher adsorption energies than Pt and Pd. Structural features of the adsorbed molecules are correlated to the calculated adsorption energies. The di-bridge[7] adsorption modes are studied in deeper detail decomposing the adsorption energies in two terms arising from molecular distortion and binding interaction to the metal. Molecular distortion is correlated to the HOMO-LUMO energy gap. The larger adsorption energies found for interactions with Rh result from the lower contribution of the distortion term. Binding interactions are described by analyzing the wave functions of naphthalene and quinoline adsorbed on a subunit of the large clusters in order to reduce the complexity of the analysis. Molecular orbitals are studied using concepts of Frontier Molecular Orbitals theory. This approach reveals that in the adsorption of naphthalene and quinoline on Pt and Pd, an antibonding state lies below the Fermi energy, while on Rh all antibonding states are empty, in agreement with the larger interaction energies. In addition, further insight is gained by projecting the density of states on the d band of the clean surfaces and of the adsorbed systems. This results in the rationalization of the structural features in terms of the concepts of electronic structure theory. The distributions of electronic density are described by means of Hirshfeld charges and isosurfaces of differential electron density. The net electron transfer from the metals to the molecules for most of the sites correlates with the trends of the adsorption energies.

Inner-shell spectroscopy by the Gaussian and augmented plane wave method

We present an approach for calculating near-edge X-ray absorption spectra at the density functional theory level, which is suited for condensed matter simulations. The method is based on the standard solution of the all-electron KS equations with a modified core-hole potential, which reproduces the relaxation of the orbitals induced by the promotion of the core electron to an unoccupied valence level. The all-electron description of the charge density is based on the Gaussian and augmented plane wave formalism. The reliability of the proposed method is assessed by comparing the computed spectra of some small molecules in the gas phase to the experimental spectra reported in literature. The sensitivity of the computed spectra to the local environment, i.e. the specific bonds formed by the absorbing atom or the presence of hydrogen bonds, open promising perspective for this technique as a predictive tool in the investigation of a more complex system of an unknown structure. The straightforward extension of the method to condensed matter is demonstrated by the calculation of the C K-edge in diamond.

Dehalogenation and Coupling of a Polycyclic Hydrocarbon on an Atomically Thin Insulator

Catalytic activity is of pivotal relevance in enabling efficient and selective synthesis processes. Recently, covalent coupling reactions catalyzed by solid metal surfaces opened the rapidly evolving field of on-surface chemical synthesis. Tailored molecular precursors in conjunction with the catalytic activity of the metal substrate allow the synthesis of novel, technologically highly relevant materials such as atomically precise graphene nanoribbons. However, the reaction path on the metal substrate remains unclear in most cases, and the intriguing question is how a specific atomic configuration between reactant and catalyst controls the reaction processes. In this study, we cover the metal substrate with a monolayer of hexagonal boron nitride (h-BN), reducing the reactivity of the metal, and gain unique access to atomistic details during the activation of a polyphenylene precursor by sequential dehalogenation and the subsequent coupling to extended oligomers. We use scanning tunneling microscopy and density functional theory to reveal a reaction site anisotropy, induced by the registry mismatch between the precursor and the nanostructured h-BN monolayer.