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Phenalenyl is a radical nanographene with triangular shape that hosts an unpaired electron with spin S = 1/2. The open-shell nature of phenalenyl is expected to be retained in covalently bonded networks. Here, we study a first step in that direction and report the synthesis of the phenalenyl dimer by combining in-solution synthesis and on-surface activation and its characterization both on Au(111) and on a monolayer of NaCl on top of Au(111) by means of inelastic electron tunneling spectroscopy (IETS). IETS shows inelastic steps that, together with a thorough theoretical analysis, are identified as the singlet-triplet excitation arising from interphenalenyl exchange. Two prominent features of our data permit to shed light on the nature of spin interactions in this system. First, the excitation energies with and without the NaCl decoupling layer are 48 and 41 meV, respectively, indicating a significant renormalization of the spin excitation energies due to exchange with the Au(111) electrons. Second, a position-dependent bias-asymmetry of the height of the inelastic steps is accounted for by an interphenalenyl hybridization of the singly occupied phenalenyl orbitals that is only possible via third neighbor hopping. This hybridization is also essential to activate kinetic interphenalenyl exchange. Our results set the stage for future work on the bottom-up synthesis of spin S = 1/2 spin lattices with large exchange interaction., Comment: 16 pages main manuscript, 4 main figures; supplementary information containing additional data is included

Strongly correlated physics arises due to electron-electron scattering within partially-filled orbitals, and in this perspective, organic molecules in open-shell configuration are good candidates to exhibit many-body effects. With a focus on neutral organic radicals with a molecular orbital hosting a single unpaired electron (SOMO) we investigate many-body effects on electron transport in a single-molecule junction setup. Within a combination of density functional theory and many-body techniques, we perform numerical simulations for an effective model for which all the parameters, including the Coulomb tensor, are derived ab-initio. We demonstrate that the SOMO resonance is prone towards splitting, and identify a giant electronic scattering rate as the driving many-body mechanism, akin to a Mott metal-to-insulator transition. The nature of the splitting, and thus of the resulting gap, as well as the spatial distribution of the SOMO and its coupling to the electrodes, have dramatic effects on the transport properties of the junction. We argue that the phenomenon and the underlying microscopic mechanism are general, and apply to a wide family of open-shell molecular systems., Comment: 15 pages, 9 figures

Localized basis sets in the projector augmented wave formalism allow for computationally efficient calculations within density functional theory (DFT). However, achieving high numerical accuracy requires an extensive basis set, which also poses a fundamental problem for the interpretation of the results. We present a way to obtain a reduced basis set of atomic orbitals through the subdiagonalization of each atomic block of the Hamiltonian. The resulting local orbitals (LOs) inherit the information of the local crystal field. In the LO basis, it becomes apparent that the Hamiltonian is nearly block-diagonal, and we demonstrate that it is possible to keep only a subset of relevant LOs which provide an accurate description of the physics around the Fermi level. This reduces to some extent the redundancy of the original basis set, and at the same time it allows one to perform post-processing of DFT calculations, ranging from the interpretation of electron transport to extracting effective tight-binding Hamiltonians, very efficiently and without sacrificing the accuracy of the results., Comment: 15 pages, 13 figures

Generating and detecting radiation in the technologically relevant range of the so-called terahertz gap ($0.1 - 10$ THz) is challenging because of a lack of efficient sources and detectors. Quantum dots in carbon nanotubes have shown great potential to build sensitive terahertz detectors usually based on photon-assisted tunnelling. A recently reported mechanism combining resonant quantum dot transitions and tunnelling barriers asymmetries results in a narrow linewidth photocurrent response with a large signal-to-noise ratio under weak THz radiation. That device was sensitive to one frequency, corresponding to transitions between equidistant quantized states. In this work we show, using numerical together with scanning tunnelling spectroscopy studies of a defect-induced metallic zigzag single-walled carbon nanotube quantum dot that simultaneously breaking various symmetries in metallic nanotube quantum dots of arbitrary chirality strongly relaxes the selection rules in the electric dipole approximation, and removes energy degeneracies. This leads to a richer set of allowed optical transitions spanning frequencies from 1 THz to several tens of THz, for a $\sim$10 nm quantum dot. Based on these findings, we propose a terahertz detector device based on a metallic single-walled carbon nanotube quantum dot defined by artificial defects. Depending on its length and contacts transparency, the operating regimes range from a high-resolution gate-tunable terahertz sensor to a broadband terahertz detector. Our calculations indicate that the device is largely unaffected by temperatures up to 100 K, making carbon nanotube quantum dots with broken symmetries a promising platform to design tunable terahertz detectors that could operate at liquid nitrogen temperatures., Comment: 23 pages, 18 figures

Strain can affect the morphology of a crystal surface, and cause modifications of its reconstruction even when weak, as in the case of mechanical bending. We carried out calculations of strain-dependent surface free energy and direct bending simulations demonstrating the change of incommensurate reconstruction in Au(111) under strain, in good agreement with recent data. Time-dependent strain should cause a sliding of the topmost layer over the second, suggesting an interesting case of nanofriction. Bending strain could also be used to fine tune the spacing of selectively absorbed nanoclusters., Comment: 4 pages, 5 figures. Published on PRB Rapid Comm. Major revision

We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural application in the study of rare events. Its capabilities are illustrated by non-trivial examples. The algorithm lends itself to straightforward parallelization, and when combined with molecular dynamics (MD) it promises to offer a powerful tool for the study of chemical reactions., Comment: 7 Pages, 4 Figures (3 in color), submitted to Phys. Rev. Lett

We propose a two-stage mechanism for the rotational surface disordering phase transition of a molecular crystal, as realized in C$_{60}$ fullerite. Our study, based on Monte Carlo simulations, uncovers the existence of a new intermediate regime, between a low temperature ordered $(2 \times 2)$ state, and a high temperature $(1 \times 1)$ disordered phase. In the intermediate regime there is partial disorder, strongest for a subset of particularly frustrated surface molecules. These concepts and calculations provide a coherent understanding of experimental observations, with possible extension to other molecular crystal surfaces., Comment: 4 pages, 2 figures

We present a calculation of the change of free energy of a solid surface upon bending of the solid. It is based on extracting the surface stress through a molecular dynamics simulation of a bent slab by using a generalized stress theorem formula, and subsequent integration of the stress with respect to strain as a function of bending curvature. The method is exemplified by obtaining and comparing free energy changes with curvature of various reconstructed Au(001) surfaces., Comment: 14 pages, 2 figures, accepted for publication in Surface Science (ECOSS-19)

Due to particle conservation, Canonical Molecular Dynamics (MD) simulations fail in the description of surface phase transitions involving coverage or lateral density changes. However, a step on the surface can act effectively as a source or a sink of atoms, in the simulation as well as in real life. A single surface step can be introduced by suitably modifying planar Periodic Boundary Conditions (PBC), to accommodate the generally inequivalent stacking of two adjacent layers. We discuss here how, through the introduction of two orthogonal surface steps, particle number conservation may no longer represent a fatal constraint for the study of these surface transitions. As an example, we apply the method for estimating temperature-induced lateral density increase of the reconstructed Au (001) surface; the resulting anisotropic cell change is consistent with experimental observations. Moreover, we implement this kind of scheme in conjunction with the variable curvature MD method, recently introduced by our group., Comment: 9 pages, 5 figures, accepted for publication in Surface Science (ECOSS-19)

Off-lattice Grand Canonical Monte Carlo simulations of the clean diamond (111) surface, based on the effective many-body Brenner potential, yield the $(2\times1)$ Pandey reconstruction in agreement with \emph{ab-initio} calculations and predict the existence of new meta-stable states, very near in energy, with all surface atoms in three-fold graphite-like bonding. We believe that the long-standing debate on the structural and electronic properties of this surface could be solved by considering this type of carbon-specific configurations., Comment: 4 pages + 4 figures, Phys. Rev. B Rapid Comm., in press (15Apr00). For many additional details (animations, xyz files) see electronic supplement to this paper at http://www.sci.kun.nl/tvs/carbon/meta.html

The large surface density changes associated with the (100) noble metals surface hex-reconstruction suggest the use of non-particle conserving simulation methods. We present an example of a surface Grand Canonical Monte Carlo applied to the transformation of a square non reconstructed surface to the hexagonally covered low temperature stable Au(100). On the other hand, classical Molecular Dynamics allows to investigate microscopic details of the reconstruction dynamics, and we show, as an example, retraction of a step and its interplay with the surface reconstruction/deconstruction mechanism., Comment: 9 pages, 5 figures, accepted for publication in Surf. Rev. and Letters (ICSOS-6)

Deposition/removal of metal atoms on the hex reconstructed (100) surface of Au, Pt and Ir should present intriguing aspects, since a new island implies hex -> square deconstruction of the substrate, and a new crater the square -> hex reconstruction of the uncovered layer. To obtain a microscopic understanding of how islands/craters form in these conditions, we have conducted simulations of island and crater growth on Au(100), whose atomistic behavior, including the hex reconstruction on top of the square substrate, is well described by mean s of classical many-body forces. By increasing/decreasing the Au coverage on Au(100), we find that island/craters will not grow unless they exceed a critical size of about 8-10 atoms. This value is close to that which explains the nonlinear coverage dependence observed in molecular adsorption on the closely related surface Pt (100). This threshold size is rationalized in terms of a transverse step correlation length, measuring the spatial extent where reconstruction of a given plane is disturbed by the nearby step., Comment: 11 pages, 5 figures, accepted for publication in Surface Science (ECOSS-18)

The reentrant layering transitions found in rare gas adsorption on solid substrates have conflictually been explained either in terms of preroughening (PR), or of top layer melting-solidification phenomena. We obtain adsorption isotherms of Lennard-Jones particles on an attractive substrate by off lattice Grand Canonical Monte Carlo (GCMC) simulation, and reproduce reentrant layering. Microscopic analysis, including layer-by-layer occupancies, surface diffusion and pair correlations, confirms the switch of the top surface layer from solid to quasi-liquid across the transition temperature. At the same time, layer occupancy is found at each jump to switch from close to full to close to half, indicating a disordered flat (DOF) surface and establishing preroughening as the underlying mechanism. Our results suggest that top layer melting is essential in triggering preroughening, which thus represents the threshold transition to surface melting in rare gas solids., Comment: 4 pages, 4 figures; accepted for publication in Phys. Rev. Letters