Scanning Tunneling Microscopy Experiments Research Articles

Structural, electronic and magnetic properties of the MnGa(111)-1 × 2 and 2 × 2 reconstructions: Spin polarized first principles total energy calculations

Using first principles total energy calculations within the periodic spin polarized density functional theory, we have investigated the structural, electronic, and magnetic properties of manganese gallium (MnGa) alloys. Specifically, we explore the MnGa(111)-1×2 and 2×2 reconstructions. The surface formation energies reveal that selected substitutions occur under Mn (Ga) rich growth conditions. Structures with top layers missing all Mn (Ga) atoms and two layers deep substitutions are also investigated. However, the formation energy shows that these structures are less favorable. For the stable structures, the magnetic properties per layer are proportional to the Mn:Ga ratio. Also, the density of states shows that the MnGa surfaces are metallic. The projected density of states shows that the electronic states in the vicinity of the Fermi level are due mainly to the manganese 3d orbitals. However charge density plots reveal that Mn 3d electrons are closer to the nucleus than Ga sp electrons. Consequently, experimental scanning tunneling microscopy images reveal periodically-arranged bright features, corresponding to the Ga atoms.

Conductance of Junctions with Acetyl-Functionalized Thiols: A First-Principles-Based Analysis

Thiol-based contacts are widely used in fabrication of molecular junctions but are associated with several drawbacks due to their chemical reactivity. In particular, their tendency to dimerize by forming sulfur–sulfur bonds is viewed as a barrier for large scale bridge fabrication. Instead, the use of functionalized sulfur end groups in the fabrication of the junctions is promoted. We analyze the effects of thiol functionalization by acetyl on the transport properties of porphyrin based bridges. In scanning tunneling microscopy (STM) experiments, where the conductance is measured as the tip is retracted, we observe molecular conductance steps due to junctions with acetyl protected thiols that are significantly lower than observed for junctions with deprotected thiols (by a factor of ≈5). Using a first-principles based computational approach, we explain the lower conductance of junctions with acetyl functionalized thiol and associate it to chemical changes of the sulfur, where essentially a tunneling barri...

Synthesis and Photochromism of Chloro‐ and tert‐Butyl‐Functionalized Terarylene Derivatives for Surface Deposition

In the field of extreme miniaturization of electronic devices, it is necessary to study candidate molecules at the single‐molecular level by scanning tunneling microscopy (STM). This necessitates molecules with specific functionalizations to control molecule–surface and molecule–molecule interactions to avoid molecular diffusion on the surface and to prevent the aggregation of molecules, respectively. In this context, we present the synthesis and photochromism of terarylene derivatives with tert‐butyl and chloride groups. We show that these groups preserve the photochemical and switching properties of the molecules. DFT calculations on the conformations of the molecules predict the presence of several conformations during vacuum‐deposition. Initial STM experiments show that tert‐butyl groups result in images with a better contrast to enable the identification of the molecules on the surface without any aggregation.

Magnetic subunits within a single molecule–surface hybrid

Magnetic molecule–surface hybrids are ideal building blocks for molecular spintronic devices due to their appealing tailorable magnetic properties and nanoscale size. So far, assemblies of interacting molecular-surface hybrids needed for spintronic functionality were generated by depositing aromatic molecules onto transition-metal surfaces, resulting in a random arrangement of hybrid magnets due to the inherent and strong hybridization. Here, we demonstrate the formation of multiple intramolecular subunits within a single molecule–surface hybrid by means of spin-polarized scanning tunneling microscopy experiments and ab initio density functional theory calculations. This novel effect is realized by depositing a polycyclic aromatic molecule on a magnetic surface. A highly asymmetric chiral adsorption position induces different structural, electronic, and magnetic properties in each aromatic ring of the molecule. In particular, the induced molecular spin polarization near the Fermi energy varies among the rings due to site- and spin-dependent molecule–surface hybridization. Our results showcase a possible organic chemistry route of tailoring geometrically well-defined assemblies of magnetically distinguishable subunits in molecule–surface hybrids.

Water-Ice Analogues of Polycyclic Aromatic Hydrocarbons: Water Nanoclusters on Cu(111).

Water has an incredible ability to form a rich variety of structures, with 16 bulk ice phases identified, for example, as well as numerous distinct structures for water at interfaces or under confinement. Many of these structures are built from hexagonal motifs of water molecules, and indeed, for water on metal surfaces, individual hexamers of just six water molecules have been observed. Here, we report the results of low-temperature scanning tunneling microscopy experiments and density functional theory calculations which reveal a host of new structures for water–ice nanoclusters when adsorbed on an atomically flat Cu surface. The H-bonding networks within the nanoclusters resemble the resonance structures of polycyclic aromatic hydrocarbons, and water–ice analogues of inene, naphthalene, phenalene, anthracene, phenanthrene, and triphenylene have been observed. The specific structures identified and the H-bonding patterns within them reveal new insight about water on metals that allows us to refine the so-called “2D ice rules”, which have so far proved useful in understanding water–ice structures at solid surfaces.

From Permeation to Cluster Arrays: Graphene on Ir(111) Exposed to Carbon Vapor.

Our scanning tunneling microscopy and X-ray photoelectron spectroscopy experiments along with first-principles calculations uncover the rich phenomenology and enable a coherent understanding of carbon vapor interaction with graphene on Ir(111). At high temperatures, carbon vapor not only permeates to the metal surface but also densifies the graphene cover. Thereby, in addition to underlayer graphene growth, upon cool down also severe wrinkling of the densified graphene cover is observed. In contrast, at low temperatures the adsorbed carbon largely remains on top and self-organizes into a regular array of fullerene-like, thermally highly stable clusters that are covalently bonded to the underlying graphene sheet. Thus, a new type of predominantly sp2-hybridized nanostructured and ultrathin carbon material emerges, which may be useful to encage or stably bind metal in finely dispersed form.

Correlating electronic and magnetic coupling in large magnetic molecules via scanning tunneling microscopy

In an effort to improve the spin coupling in single-molecule magnets, we rationally designed a new building-block molecule with significantly enhanced spin coupling compared to a previously established molecule. We relate this to a stabilization of aromaticity in the central connecting carbon ring, promoting the spin-polarization mechanism. This correlation between magnetic and electronic properties is supported by bulk measurements as well as submolecularly resolved scanning tunneling microscopy and spectroscopy experiments, where we found distinct differences in the local density of states distribution of the two molecules, especially at the central carbon ring. While the established molecule exhibits localized, spatially decoupled and even switchable states, the improved building block exhibits symmetric local density of states delocalized over the entire molecule, also revealing that this main characteristic electronic property is preserved upon adsorption on a metal surface. Due to their planar geometry, these molecules can serve as model systems for scanning-probe based studies of molecular magnetism.

Influence of Halogen Bonds on the Compactness of Supramolecular Assemblies on Si(111)-B

The role of halogen bonds on the molecular structure of large assemblies on a weakly reactive surface has been investigated. Our scanning tunneling microscopy (STM) experiments reveal a large variation of compactness of assemblies along the amount of halogen bonds within the building unit. In brief, we observe an increasing compactness of the supramolecular structures for zero, one, and two halogen atoms per molecule. Our experimental results are supported by molecular and STM calculations where the presence of van der Waals interactions was also considered. We found that molecular units adopt a structural arrangement that maximizes highly selective nitrogen-surface bonding and favor lateral interactions where the molecules are driven by halogen bonds. This study suggests that the presence of halogen bonds can be an efficient tool to control the molecular arrangement within two-dimension or one-dimension supramolecular networks on a silicon surface.

Size-dependent dissociation of small cobalt clusters on ultrathin NaCl films

Mass-selected anionic cobalt clusters of two different sizes (Co2 and Co13) were deposited onto ultrathin NaCl films grown on an Au(111) substrate. Using scanning tunneling microscopy experiments and density functional theory simulations, we show that the deposited Co2 cluster dissociates and that the resulting Co atoms dope the NaCl surface by substituting Na ions. In contrast, the larger Co13 cluster does not dissociate and remains stable on top of the NaCl film. The size-dependent fragmentation of clusters is an important aspect in the understanding of the chemical interaction between size-selected small aggregates of atoms and supporting surfaces.

Investigation of the structural anisotropy in a self-assembling glycinate layer on Cu(100) by scanning tunneling microscopy and density functional theory calculations

Self-assembling organic molecule-metal interfaces exhibiting free-electron like (FEL) states offers an attractive bottom-up approach to fabricating materials for molecular electronics. Accomplishing this, however, requires detailed understanding of the fundamental driving mechanisms behind the self-assembly process. For instance, it is still unresolved as to why the adsorption of glycine ([NH2(CH2)COOH]) on isotropic Cu(100) single crystal surface leads, via deprotonation and self-assembly, to a glycinate ([NH2(CH2)COO–]) layer that exhibits anisotropic FEL behavior. Here, we report on bias-dependent scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations for glycine adsorption on Cu(100) single crystal surface. We find that after physical vapor deposition (PVD) of glycine on Cu(100), glycinate self-assembles into an overlayer exhibiting c(2×4) and p(2×4) symmetries with non-identical adsorption sites. Our findings underscore the intricacy of electrical conductivity in nanomolecular organic overlayers and the critical role the structural anisotropy at molecule-metal interface plays in the fabrication of materials for molecular electronics.

Epitaxial growth and structure of monolayer cerium oxide films on Rh(111)

We prepared monolayer cerium (Ce) oxide films on Rh(111) to investigate their growth and structure using scanning tunneling microscopy (STM), low-energy electron diffraction, X-ray photoemission spectroscopy (XPS), and density functional theory (DFT) calculations. For quantitative analysis of Ce-oxide films, we used the combined techniques of XPS and Rutherford backscattering spectrometry to determine the concentration of Ce and O atoms. We prepared a monolayer (ML) Ce-oxide film by annealing a metallic Ce film at 0.3ML coverage in an oxygen atmosphere. A well-ordered Ce-oxide phase with a (4×4) unit cell was obtained. The epitaxially grown Ce-oxide film aligned along the 〈110〉 azimuthal direction of Rh(111). The number of Ce and O atoms in the (4×4) unit cell was estimated. The STM images indicated that the two-dimensional island growth of the p(4×4) phase with p3m1 symmetry can be explained using the missing Ce atoms model. A simulated STM image of the p(4×4) structural model was in good agreement with the experimental STM image. The formation of Ce-oxide films on Rh(111) at submonolayer coverage was discussed on the basis of the results of DFT+U calculations.

Metal-insulator (fermion-boson)-crossover origin of pseudogap phase of cuprates I: anomalous heat conductivity, insulator resistivity boundary, nonlinear entropy

Among all experimental observations of cuprate physics, the metal-insulator-crossover (MIC), seen in the pseudogap (PG) region of the temperature-doping phase diagram of copper-oxides under a strong magnetic field, when the superconductivity is suppressed, is most likely the most intriguing one. Since it was expected that the PG-normal state for these materials, as for conventional superconductors, is conducting. This MIC, revealed in such phenomena as heat conductivity downturn, anomalous Lorentz ratio, insulator resistivity boundary, nonlinear entropy, resistivity temperature upturn, insulating ground state, nematicity- and stripe-phases and Fermi pockets, unambiguously indicates on the insulating normal state, from which the high-temperature superconductivity (HTS) appears. In the present work (article I), we discuss the MIC phenomena mentioned in the title of article. The second work (article II) will be devoted to discussion of other listed above MIC phenomena and also to interpretation of the recent observations in the hidden magnetic order and scanning tunneling microscopy (STM) experiments spin and charge fluctuations as the intra PG and HTS pair ones. We find that all these MIC (called in the literature as non-Fermi liquid) phenomena can be obtained within the Coulomb single boson and single fermion two liquid model, which we recently developed, and the MIC is a crossover of single fermions into those of single bosons. We show that this MIC originates from bosons of Coulomb two liquid model and fermions, whose origin is these bosons. At an increase of doping up to critical value or temperature up to PG boundary temperature, the boson system undegoes bosonic insulator - bosonic metal - fermionic metal transitions.

Chemisorption of a Strained but Flexible Molecule: Cyclooctyne on Si(001).

The adsorption characteristics of a promising system for hybrid organic-inorganic interfaces, cyclooctyne on Si(001), is analyzed using density functional theory. The chemisorbed 'on-top' configuration, where a cycloadduct is formed between the ring triple bond and a surface dimer, is shown to be most stable. Less stable are 'bridge' and 'sublayer' modes featuring two molecule-surface bonds and the 'pedestal' mode with four bonds. Investigations with our recently proposed periodic energy decomposition analysis (pEDA) reveal that the four-bond configuration is destabilized by large deformation energies needed within molecule and surface as well as rather weak molecule-surface bonds. Dispersion interactions show significant influence on energy and structure of the configurations leading to an increased bending of the rather flexible molecules. Thus, features found in previous scanning tunneling microscopy experiments are conclusively explained with bent 'on-top' configurations and the 'pedestal' mode can be ruled out. A comparison to acetylene shows that the ring structure and the resulting strain of cyclooctyne are responsible for an increased reactivity of the larger adsorbate due to a pre-forming of the ring triple bond for surface bonding. In contrast, ring strain leads only to negligible electronic effects on the adsorbate-surface bonds. The computations highlight the need for in-depth theoretical analysis to understand adsorption characteristics of large, flexible molecules.

Strength of effective Coulomb interactions and origin of ferromagnetism in hydrogenated graphene

Hydrogenation provides a novel way to tune the electronic properties of graphene. Recent scanning tunneling microscopy experiments have demonstrated that local graphene magnetism can be selectively switched on and off by hydrogen (H) dimers. Employing first-principles calculations in conjunction with the constrained random-phase approximation we determine the strength of the effective Coulomb interaction $U$ in hydrogenated graphene. We find that the calculated $U$ parameters are smaller than the ones in graphene and depend on the H concentration. Moreover, the $U$ parameters are very sensitive to the position of H atoms adsorbed on the graphene lattice. We discuss the instability of the paramagnetic state of the hydrogenated graphene towards the ferromagnetic one on the basis of calculated $U$ parameters within the Stoner model. Spin-polarized calculations reveal that the itinerant ferromagnetism in hydrogenated graphene can be well accounted for by the Stoner model.

Adsorption of PTCDA on Ge(001)

Adsorption of 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) on the Ge(001) surface was studied using scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and the density-functional theory (DFT) calculations. Only single adsorption configuration of the PTCDA molecule was observed at low coverages on the Ge(001) at room temperature, unlike on the Si(001) where several adsorption configurations were reported. This indicates that the PTCDA molecules on the Ge(001) were more mobile than those on the Si(001). Atomic structure of the adsorption configuration on the Ge(001) was determined by comparison between the STM experiments and the DFT calculations. Bias-dependent STM images, STS, and calculated projected density of state curves show nontrivial hybridization of molecular orbitals with surface states of the Ge substrate. Interactions of the PTCDA molecule with the Ge and the Si surfaces were in detail analyzed by the DFT calculation, considering five main competing contributions to the adsorption energy: formation energy of polar covalent Ge–O (Si–O) bonds, energy of molecular deformation, interaction energy of Ge atoms with the perylene core of PTCDA, energy of dimer buckling deformation, and van der Waals interaction energy. The analysis explains different adsorption behaviors between the Ge and the Si substrates.

STM Study of Ketopantolactone/(R)-1-(1-Naphthyl)ethylamine Complexes on Pt(111): Comparison of Prochiral and Enantiomeric Ratios and Examination of the Contribution of CH···OC Bonding

We report a comprehensive model surface science study, using scanning tunneling microscopy (STM), of the regioselective and stereospecific complexation of a prochiral substrate molecule to a chiral modifier molecule on a metal surface. The system is chosen so as to compare the prochiral ratio (pr) measured directly by STM for the model system with the reported enantiomeric ratio (er) for the hydrogenation of the prochiral molecule using the same chiral modifier and metal under true reaction conditions. Specifically, diastereomeric complexes formed between ketopantolactone (KPL) and (R)-1-(1-naphthyl)ethylamine ((R)-NEA) on Pt(111) were studied as a function of the ratio of KPL to (R)-NEA. Only KPL molecules in complexes are detected in the STM experiments, performed between 237 and 250 K, due to rapid diffusion of free KPL on the surface. The prochirality of KPL in almost all bimolecular and termolecular, (KPL)2/(R)-NEA, complexation configurations is assigned as pro-R or pro-S using the contrast within t...

Local resilience of the 1T−TiSe2 charge density wave to Ti self-doping

In Ti-intercalated self-doped $1T$-TiSe$_2$ crystals, the charge density wave (CDW) superstructure induces two nonequivalent sites for Ti dopants. Recently, it has been shown that increasing Ti doping dramatically influences the CDW by breaking it into phase-shifted domains. Here, we report scanning tunneling microscopy and spectroscopy experiments that reveal a dopant-site dependence of the CDW gap. Supported by density functional theory, we demonstrate that the loss of the longrange phase coherence introduces an imbalance in the intercalated-Ti site distribution and restrains the CDW gap closure. This local resilient behavior of the $1T$-TiSe$_2$ CDW reveals a novel mechanism between CDW and defects in mutual influence.

What can be inferred from moiré patterns? A case study of trimesic acid monolayers on graphite.

Self-assembly of benzene-1,3,5-tricarboxylic acid (trimesic acid - TMA) monolayers at the alkanoic acid-graphite interface is revisited. Even though this archetypal model system for hydrogen bonded porous networks is particularly well studied, the analysis of routinely observed superperiodic contrast modulations known as moiré patterns lags significantly behind. Fundamental questions remain unanswered such as, are moiré periodicity and orientation always the same, i.e. is exclusively only one specific moiré pattern observed? What are the geometric relationships (superstructure matrices) between moiré, TMA, and graphite lattices? What affects the moiré pattern formation? Is there any influence from solvent, concentration, or thermal treatment? These basic questions are addressed via scanning tunneling microscopy experiments at the liquid-solid interface, revealing a variety of different moiré patterns. Interestingly, TMA and graphite lattices were always found to be ∼5° rotated with respect to each other. Consequently, the observed variation in the moiré patterns is attributed to minute deviations (<2°) from this preferred orientation. Quantitative analysis of moiré periods and orientations facilitates the determination of the TMA lattice parameter with picometer precision.

Chemically induced topological zero mode at graphene armchair edges.

The electronic and magnetic properties of chemically modified graphene armchair edges are studied using a combination of tight-binding calculations, first-principles modelling, and low temperature scanning tunneling microscopy (STM) experiments. The atomically resolved STM images of the hydrogen etched graphitic edges suggest the presence of localized states at the Fermi level for certain armchair edges. We demonstrate theoretically that the topological zero-energy edge mode may emerge at armchair boundaries with asymmetrical chemical termination of the two outermost atoms in the unit cell. We particularly focus our attention on armchair edges terminated by various combinations of the hydrogen (H, H2) and methylene (CH2) groups. The inclusion of the spin component in our calculations reveals the appearance of π-electron-based magnetism at the armchair edges under consideration.

Insulated molecular wires: inhibiting orthogonal contacts in metal complex based molecular junctions.

Metal complexes are receiving increased attention as molecular wires in fundamental studies of the transport properties of metal|molecule|metal junctions. In this context we report the single-molecule conductance of a systematic series of d8 square-planar platinum(ii) trans-bis(alkynyl) complexes with terminal trimethylsilylethynyl (C[triple bond, length as m-dash]CSiMe3) contacting groups, e.g. trans-Pt{C[triple bond, length as m-dash]CC6H4C[triple bond, length as m-dash]CSiMe3}2(PR3)2 (R = Ph or Et), using a combination of scanning tunneling microscopy (STM) experiments in solution and theoretical calculations using density functional theory and non-equilibrium Green's function formalism. The measured conductance values of the complexes (ca. 3-5 × 10-5G0) are commensurate with similarly structured all-organic oligo(phenylene ethynylene) and oligo(yne) compounds. Based on conductance and break-off distance data, we demonstrate that a PPh3 supporting ligand in the platinum complexes can provide an alternative contact point for the STM tip in the molecular junctions, orthogonal to the terminal C[triple bond, length as m-dash]CSiMe3 group. The attachment of hexyloxy side chains to the diethynylbenzene ligands, e.g. trans-Pt{C[triple bond, length as m-dash]CC6H2(Ohex)2C[triple bond, length as m-dash]CSiMe3}2(PPh3)2 (Ohex = OC6H13), hinders contact of the STM tip to the PPh3 groups and effectively insulates the molecule, allowing the conductance through the full length of the backbone to be reliably measured. The use of trialkylphosphine (PEt3), rather than triarylphosphine (PPh3), ancillary ligands at platinum also eliminates these orthogonal contacts. These results have significant implications for the future design of organometallic complexes for studies in molecular junctions.