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Several studies have addressed the presence of unexpected components in the molecular level X-ray Photoelectron Spectroscopy (XPS) spectra, specially in the N1s signal, when tetrapyrrole molecules are deposited on different surfaces in Ultra High Vacuum (UHV) conditions. In this work, we employ a set of DFT-based tools to unravel the origin of an unpredicted peak in the N1s core level spectra of metal phthalocyanines (in particular, ZnPc) adsorbed on Cu(110). We analyze the different possible chemical or electronic mechanisms that might explain this experimental result. On one hand, we prove that surface effects, such as LUMO splitting and surface screening, cannot account for the huge experimental CLSs. On the other hand, we show that, when adsorbed at low temperatures, these molecules capture residual H atoms from the surface, giving rise to hydrogenated molecular species without de-metalation of the molecule and, thus, to an extra component in the molecular CLS spectra. Only upon annealing, and subsequent H release, do the molecules recover their nominal structural and electronic properties. Our results thus demonstrate that residual hydrogen, which is known to be the primary residual gas in UHV systems, might have a significant effect on the measured electronic properties of molecule-surface complexes.

Understanding grain boundaries in polycrystalline graphene is crucial for the control of both their electronic and mechanical properties. Depending on their topological structure, boundaries can impede transport across grains, or host their own one dimensional metallic states. Concerning mechanical stability, they can either weaken or strengthen the graphene sheet. We here report experimental evidence on some predicted and other new topological defect boundary structures, as found by Scanning Tunnelling Microscopy (STM) in graphene nanoislands grown on Ni(111) by CVD. By using mild annealing temperatures, we obtain multi-domain nanoislands with different types of domain boundaries. High-resolution STM images allow us to characterize both the stacking and orientation of graphene domains and the boundary atomic structure. From a statistical analysis of the rotated domains, we conclude that their abundance is closely related to the boundary energetics, evidencing that the selection of rotational domains is determined by boundary rather than stacking energetics. linear and ring boundaries separating 30º rotated domains are particularly interesting: the linear ones are predicted to be transparent to Dirac electrons, whereas confined resonances have already been observed in quantum dots bound by similar ring boundaries.

We report the energy level alignment evolution of valence and conduction bands of armchair-oriented graphene nanoribbons (aGNR) as their band gap shrinks with increasing width. We use 4,4″-dibromo-para-terphenyl as the molecular precursor on Au(111) to form extended poly-para-phenylene nanowires, which can subsequently be fused sideways to form atomically precise aGNRs of varying widths. We measure the frontier bands by means of scanning tunneling spectroscopy, corroborating that the nanoribbon's band gap is inversely proportional to their width. Interestingly, valence bands are found to show Fermi level pinning as the band gap decreases below a threshold value around 1.7 eV. Such behavior is of critical importance to understand the properties of potential contacts in GNR-based devices. Our measurements further reveal a particularly interesting system for studying Fermi level pinning by modifying an adsorbate's band gap while maintaining an almost unchanged interface chemistry defined by substrate and adsorbate.

A set of density-functional theory based tools is employed to elucidate the influence of chemical and surface-induced changes on the core level shifts of X-ray photoelectron spectroscopy experiments. The capabilities of our tools are demonstrated by analyzing the origin of an unpredicted component in the N 1s core level spectra of metal phthalocyanine molecules (in particular ZnPc) adsorbed on Cu(110). We address surface induced effects, such as splitting of the lowest unoccupied molecular orbital or local electrostatic effects, demonstrating that these cannot account for the huge core level shift measured experimentally. Our calculations also show that, when adsorbed at low temperatures, these molecules might capture hydrogen atoms from the surface, giving rise to hydrogenated molecular species and, consequently, to an extra component in the molecular core level spectra. Only upon annealing, and subsequent hydrogen release, would the molecules recover their nominal structural and electronic properties.

Bottom-up chemical reactions of selected molecular precursors on a gold surface can produce high quality graphene nanoribbons (GNRs). Here, we report on the formation of quantum dots embedded in an armchair GNR by substitutional inclusion of pairs of boron atoms into the GNR backbone. The boron inclusion is achieved through the addition of a small amount of boron substituted precursors during the formation of pristine GNRs. In the pristine region between two boron pairs, the nanoribbons show a discretization of their valence band into confined modes compatible with a Fabry–Perot resonator. Transport simulations of the scattering properties of the boron pairs reveal that they selectively confine the first valence band of the pristine ribbon while allowing an efficient electron transmission of the second one. Such band-dependent electron scattering stems from the symmetry matching between the electronic wave functions of the states from the pristine nanoribbons and those localized at the boron pairs.

Construction of single-molecule electronic devices requires the controlled manipulation of organic molecules and their properties. This could be achieved by tuning the interaction between the molecule and individual atoms by local “on-surface” chemistry, i.e., the controlled formation of chemical bonds between the species. We demonstrate here the reversible attachment of a planar conjugated polyaromatic molecule to a pair of unpassivated dangling bonds on a hydrogenated Ge(001):H surface via a Diels–Alder [4+2] addition using the tip of a scanning tunneling microscope (STM). Due to the small stability difference between the covalently bonded and a nearly undistorted structure attached to the dangling bond dimer by long-range dispersive forces, we show that at cryogenic temperatures the molecule can be switched between both configurations. The reversibility of this covalent bond forming reaction may be applied in the construction of complex circuits containing organic molecules with tunable properties.

Controlling the strength of the coupling between organic molecules and single atoms provides a powerful tool for tuning electronic properties of single-molecule devices. Here, using scanning tunneling microscopy and spectroscopy (STM/STS) supported by theoretical modeling, we study the interaction of a planar organic molecule (trinaphthylene) with a hydrogen-passivated Ge(001):H substrate and a single dangling bond quantum dot on that surface. The electronic structure of the molecule adsorbed on the hydrogen-passivated surface is similar to the gas phase structure and the measurements show that HOMO and LUMO states contribute to the STM filled and empty state images, respectively. Furthermore, we show that the electronic properties are not significantly affected when the molecule is attached to the single dangling bond, which is in contrast with the strong interaction of the molecule with a dangling bond dimer. Our results show that the dangling bond quantum dots could stabilize organic molecules on a hydrogenated semiconductor without affecting their originally designed gas phase electronic properties. Together with the ability to laterally manipulate the molecules on the surface, this will be advantageous in the construction of single-molecule devices, where the coupling and positioning of the molecules on the substrate could be tuned by a proper design of the surface quantum dot arrays, comprising both single and dimerized dangling bonds.

Contributing to the need for new graphene nanoribbon (GNR) structures that can be synthesized with atomic precision, we have designed a reactant that renders chiral (3,1)-GNRs after a multistep reaction including Ullmann coupling and cyclodehydrogenation. The nanoribbon synthesis has been successfully proven on different coinage metals, and the formation process, together with the fingerprints associated with each reaction step, has been studied by combining scanning tunneling microscopy, core-level spectroscopy, and density functional calculations. In addition to the GNR’s chiral edge structure, the substantial GNR lengths achieved and the low processing temperature required to complete the reaction grant this reactant extremely interesting properties for potential applications.

We have theoretically investigated the electronic properties of neutral and n-doped dangling bond (DB) quasi-one-dimensional structures (lines) in the Si(001):H and Ge(001):H substrates with the aim of identifying atomic-scale interconnects exhibiting metallic conduction for use in on-surface circuitry. Whether neutral or doped, DB lines are prone to suffer geometrical distortions or have magnetic ground states that render them semiconducting. However, from our study we have identified one exception—a dimer row fully stripped of hydrogen passivation. Such a DB-dimer line shows an electronic band structure which is remarkably insensitive to the doping level, and thus, it is possible to manipulate the position of the Fermi level, moving it away from the gap. Transport calculations demonstrate that the metallic conduction in the DB-dimer line can survive thermally induced disorder but is more sensitive to imperfect patterning. In conclusion, the DB-dimer line shows remarkable stability to doping and could serve as a one-dimensional metallic conductor on n-doped samples.

Recently, it has been reported theoretically a current switching mechanism by voltage control in a system made by two perpendicular 14-armchair graphene nanoribbons (GNRs). In order to investigate the possibilities of using crossed GNRs as ON/OFF devices, we have studied their electronic and transport properties as function structural parameters determining the crossing. Our calculations were performed with TranSIESTA code, which has been recently generalized to consider N >= 1 arbitrarily distributed electrodes at finite bias. We find that the transmission along each individual GNR and among them strongly depends on the stacking. For a 60º rotation angle, the lattice matching in the crossing region provokes a strong scattering effect that translates into an increased interlayer transmission.

Controlling the coupling between single-molecules and dangling-bonds (DBs) on hydrogenpassivated semiconductor surfaces is of relevance from both technological and fundamental perspectives. Furthermore, DBs can be patterned on these surfaces with atomic precision by STM tip induced desorption of the hydrogen atoms from the passivated layer. This opens up the possibility to tune the properties of the molecules by contacting them with DB arrays of different complexity. With this in mind, we have investigated the interaction of a conjugated polyaromatic molecule (trinaphthylene, Y molecule) with a single-DB or a DB dimer on the hydrogenated Ge(001):H surface. Using Scanning Tunneling Microscope (STM) and Spectroscopy (STS) experiments combined with theoretical calculations, we have found significantly different results in each case. Y molecules interact weakly with the hydrogen-passivated surface, and are nearly decoupled from the substrate states. As a result, the electronic structure of the molecule positioned on the single DB is similar to the gas phase electronic structure. On the contrary, the formation of chemical bonds following the Diels-Alder addition for Y molecules attached to surface DB dimers results in a significant change of the molecular electronic structure. Our results show that the strength of the coupling between the molecule and the substrate could be tuned by creating complex arrays comprising both single and dimerized DBs.

Bottom-up processes involving the coupling of molecular precursors enable synthesizing atomically precise, functionalized graphene nanoribbons (GNR). This in turn opens up a new route to tailor the electronic and chemical properties of GNRs. Here we present a comparative study on the growth, structural characterization and chemical stability of zig-zag shaped functionalized GNRs obtained by the surface-assisted coupling of specifically synthesized molecular precursors on the Au(111) surface (Figure 1 a, b). Scanning tunneling microscopy (STM) shows that these precursors lead to straight and almost defect free GNRs (Figure 1c). By means of X-ray photoelectron spectroscopy (XPS) we are able to follow the different reaction steps (namely debromination and cyclodehydrogenation) resulting in the synthesis of the nanoribbons. Moreover, the combination of the two techniques allows us to check the chemical stability of the functional radicals, observing, in particular, that the methoxy group, though not surviving to the cyclodehydrogenation reaction, differently from the fluorine radical, still strongly affects the formation and self-assembly of the nanoribbons on the surface.

Graphene Nanoribbons (GNRs) are one dimensional stripes of graphene. Their electronic and magnetic properties depend on their width and edge structure. Armchair graphene nanoribbons (AGNRs) have a width dependent electronic gap which makes them suitable for applications in carbon-based nanoelectronics. On-surface reaction of halogenated bianthracene (DBBA) monomers is one of the most successful processes to tailor the dimensions and the edges of GNRs with atomic precision. Chemical modification of these precursors provides a tool to modify the electronic structure of AGNR, and obtain band gaps in a range suitable for semiconducting and optoelectronic applications. In this work we grow boron doped 7-AGNRs with boron atom pairs substituents along the GNR backbone (2B-7-AGNR) on Au(111) and Au(223) surfaces by using chemically modified DBBA molecules. By means of LT-STM, ARPES and DFT calculations we characterize in detail the electronic structure of 2B-7-AGNR. We find that B atoms, closer to the Au surface than carbons, induce a strong p-doping of 7-AGNRs valence band. The diboron backbone induces the formation of a new conduction band that results from the hybridization of the borns pz states and the Au surface state. The band gap for 2B-7-AGNR measured by STS amounts to ~0.9 eV, almost 40% less than the pristine 7-AGNR.

We present a combined experimental and theoretical study of the electronic properties of close-spaced dangling-bond (DB) pairs in a hydrogen-passivated Si(001):H p-doped surface. Two types of DB pairs are considered, called >cross> and >line> structures. Our scanning tunneling spectroscopy (STS) data show that, although the spectra taken over different DBs in each pair exhibit a remarkable resemblance, they appear shifted by a constant energy that depends on the DB-pair type. This spontaneous asymmetry persists after repeated STS measurements. By comparison with density functional theory (DFT) calculations, we demonstrate that the magnitude of this shift and the relative position of the STS peaks can be explained by distinct charge states for each DB in the pair. We also explain how the charge state is modified by the presence of the scanning tunneling microscopy (STM) tip and the applied bias. Our results indicate that, using the STM tip, it is possible to control the charge state of individual DBs in complex structures, even if they are in close proximity. This observation might have important consequences for the design of electronic circuits and logic gates based on DBs in passivated silicon surfaces.

We combine experimental observations by scanning tunneling microscopy (STM) and density functional theory (DFT) to reveal the most stable edge structures of graphene on Ni(111) as well as the role of stacking-driven activation and suppression of edge reconstruction. Depending on the position of the outermost carbon atoms relative to hollow and on-top Ni sites, zigzag edges have very different energies. Triangular graphene nanoislands are exclusively bound by the more stable zigzag hollow edges. In hexagonal nanoislands, which are constrained by geometry to alternate zigzag hollow and zigzag top edges along their perimeter, only the hollow edge is stable, whereas the top edges spontaneously reconstruct into the (57) pentagon–heptagon structure. Atomically resolved STM images are consistent with either top-fcc or top-hcp epitaxial stacking of graphene and Ni sites, with the former being favored by DFT. Finally, we find that there is a one-to-one relationship between the edge type, graphene stacking, and orientation of the graphene islands.

The actual demand of increasingly smaller devices drives the endeavors to explore new methods to miniaturize the designs. Thus, developments to produce ordered nanostructured surfaces are stimulating fields. In this context, a novedous molecular/substrate interaction mechanism that derives in a unique adsorbate induced surface reconstruction is presented. In particular we show how metalated phthalocyanines can promote the formation of regular arrays of Cu nanoribbons on its (110) surface. At variance with the conventional changes of metal reconstructions upon molecular adsorption observed so far, the presented faceting is found to involve a massive reorganization of Cu adatoms. The energy gain of the final system comes not only from the preferential adsorption position of phthalocyanines on the copper surface, but also from their interaction with the surrounded adatoms. By combining experimental (Scanning Tunneling Microcopy) and theoretical surface science techniques we demonstrate that indeed the mechanism behind the massive surface reshaping involves a molecular mediated uni-directional blocking of diffusing surface adatoms. Optimization of the organization involves extra adatoms trapped between molecules.