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We uncover the electronic structure of molecular graphene produced by adsorbed CO molecules on a copper (111) surface by means of first-principles calculations. Our results show that the band structure is fundamentally different from that of conventional graphene, and the unique features of the electronic states arise from coexisting honeycomb and Kagome symmetries. Furthermore, the Dirac cone does not appear at the K-point but at the Γ-point in the reciprocal space and is accompanied by a third, almost flat band. Calculations of the surface structure with Kekule distortion show a gap opening at the Dirac point in agreement with experiments. Simple tight-binding models are used to support the first-principles results and to explain the physical characteristics behind the electronic band structures.

The formation of extended electron states in one-dimensional nanostructures is of key importance for the function of molecular electronics devices. Here we study the effects of strong electron-phonon interaction on the formation of extended electronic states in intentionally created Cl vacancy pairs and chains in a NaCl bilayer on Cu(111). The interaction between the vacancies was tailored by fabricating vacancy pairs and chains of different orientation and separation with atomic precision using vertical manipulation. Small separation of divacancies led to the formation of symmetric and antisymmetric vacancy states and localized interface-states. By scanning tunneling spectroscopy (STS) we measured their energy splitting and broadening as a function of the inter-vacancy separation. Unexpectedly, the energy splitting between the vacancy states is enlarged by level repulsion resulting from phonon dressing of the electronic states, as evidenced by theory. Already for a few coupled vacancies we observe an emerging band structure of the defect band., 9 pages, 4 figures

We study tip-adsorbate–substrate interactions in scanning tunneling microscopy (STM) manipulation and imaging, and the influence of impurities on the images. Thence, we perform molecular dynamics simulations and calculate qualitative STM images for oxygen on Pt(1 1 1) surface. The adsorption site of the oxygen molecule is found to be in accordance with ab initio calculations. The calculated STM image has a good resemblance to the experimental ones. The contamination of the tip by oxygen or water alters the STM image strongly. Molecular dynamics simulations on manipulations of oxygen on the surface reveal several mechanisms of how molecular oxygen can be either produced or decomposed with STM tip. Finally, we find out that transfer of oxygen from the surface to an STM tip is not very probable.

Man-made artificial graphene has attracted significant attention in the past few years due to the possibilities to construct designer Dirac fermions with unexpected topological properties and applications in nanoelectronics. Here we use a first-principles approach within density-functional theory to study molecular graphene similar to the experiment by Gomes~{\em et al.}, Nature {\bf 483}, 306 (2012). The system comprises carbon monoxide molecules arranged on a copper (111) surface in such a way that a hexagonal lattice is obtained with the characteristic electronic properties of graphene. Our results show in detail how carbon monoxide molecules modify the copper surface (and regions beneath) and create a hexagonal lattice of accumulated electrons between the adsorbate molecules. We also demonstrate how the properties of the formed Dirac fermions change as the CO density is tuned, and provide a direct comparison with experimental scanning tunneling microscope images.

We present scanning tunneling microscopy (STM)-based single-molecule synthesis of linear metal−ligand complexes starting from individual metal atoms (iron or nickel) and organic molecules (9,10-dicyanoanthracene) deposited on an ultrathin insulating film. We directly visualize the frontier molecular orbitals by STM orbital imaging, from which, in conjunction with detailed density functional theory calculations, the electronic structure of the complexes is inferred. Our studies show how the order of the molecular orbitals and the spin-state of the complex can be engineered through the choice of the metal atom. The high-spin iron complex has a singly occupied delocalized orbital with a large spin-splitting that points to the use of these engineered complexes as modular building blocks in molecular spintronics.

We present a fast and efficient tight-binding (TB) method for simulating scanning tunneling microscopy (STM) imaging of adsorbate molecules on ultrathin insulating films. Due to the electronic decoupling of the molecule from the metal surface caused by the presence of the insulating overlayer, the STM images of the frontier molecular orbitals can be simulated using a very efficient scheme, which also enables the analysis of phase shifts in the STM current. Au-pentacene complex adsorbed on a NaCl bilayer on Cu substrate provides an intricate model system, which has been previously studied both experimentally and theoretically. Our calculations indicate that the complicated shape of the molecular orbitals may cause multivalued constant current surfaces -- leading to ambiguity of the STM image. The results obtained using the TB method are found to be consistent with both DFT calculations and experimental data., 19 pages, 5 figures

A combined study using density functional calculations and scanning tunneling microscopy experiments shows that individual silver adatoms on ultrathin sodium chloride films on copper surfaces are stable in three different charge states—neutral, negatively, and positively charged adatoms. The charge states of the individual adatoms were manipulated by voltage pulses. The key parameters determining the stability of various charge states are identified and discussed within a simple model.

A covalent bond between an individual pentacene molecule and a gold atom was formed by means of single-molecule chemistry inside a scanning tunneling microscope junction. The bond formation is reversible, and different structural isomers can be produced. The single-molecule synthesis was done on ultrathin insulating films that electronically isolated the reactants and products from their environment. Direct imaging of the orbital hybridization upon bond formation provides insight into the energetic shifts and occupation of the molecular resonances.

Broad Gaussian line shapes are observed in scanning tunneling spectroscopy of single, localized electronic states induced by Cl vacancies in ultrathin NaCl films on Cu surfaces. Using a simple inelastic resonance tunneling model, we show that the observed broad line shapes are caused by a strong coupling between the localized state and the optical phonons in the film. The parameters for the model are obtained from density functional calculations, in which the occupation of the vacancy state temporarily taking place in the experiment has also been accounted for.

We compare computer simulations to experimental scanning tunneling microscopy (STM) images of chloronitrobenzene molecules on a Cu(111) surface. The experiments show that adsorption induced isomerization of the molecules takes place on the surface. Furthermore, not only the submolecular features can be seen in the STM images, but different isomers can also be recognized. The Todorov-Pendry approach to tunneling produces simulated STM images which are in good accordance with the experiments. Alongside with STM simulations in a tight-binding basis, ab initio calculations are performed in order to analyze the symmetry of relevant molecular orbitals and to consider the nature of tunneling channels. Our calculations show that while the orbitals delocalized to the phenyl ring create a relatively transparent tunneling channel, they also almost isolate the orbitals of the substitute groups at energies which are relevant in STM experiments. These features of the electronic structure are the key ingredients of the accurate submolecular observations.

A change in bias voltage can reverse the contrast of a scanning-tunneling microscopy (STM) image of an adsorbate molecule on a solid surface. This contrast change may take place not only in a case of tunneling in the neighborhood of a resonance level of the adsorbate, but it can also be seen in the case of a wide energy gap between highest occupied molecular-orbital and lowest unoccupied molecular-orbital levels. In order to find a unified description of contrast changes in STM images, we make comparisons between different approaches to tunneling. We especially consider the role of phase differences between possible tunneling channels. These phase differences can be related to the imaginary and real parts of the Green's function of the system which reveal whether the tunneling takes place through a resonant state or a forbidden gap. Finally, we compare experimental and calculated images of oxygen molecules on a silver surface and analyze the mechanisms of the contrast change in terms of phase shifts in different tunneling channels.

We perform a molecular dynamics (MD) study of non-dissociative adsorption of O 2 molecule on Pt{111} surface at low temperatures, and analyse the STM image of the obtained geometry. The interatomic forces for the simulation are calculated using tight-binding method in density matrix formalism with the constraint of local charge neutrality. The STM image is constructed by calculating tunneling current between a sharp metal tip and the sample. The MD simulation gives an adsorption site with a very plausible bonding behaviour. Furthermore, the corresponding STM image is similar to recent experimental images. The present simulation suggests formation of a larger complex of the oxygen molecule and two Pt atoms. It turns out that the STM image does not directly show the orientation of the O 2 molecule, and has such a complicated origin in interference of atomic orbitals of the formed complex, that an optimization of the surface structure using MD simulation, instead of intuitive considerations, is necessary.