STM investigations of PTCDA and PTCDI on graphite and MoS2. A systematic study of epitaxy and STM image contrast

Monolayers of the organic molecules perylene-3,4,9,10-tetra-carboxylic-dianhydride (PTCDA) and diimide (PTCDI) on graphite and MoS₂ have been imaged with scanning tunneling microscopy. The epitaxial growth of the two molecules is determined by the intermolecular interaction but nearly independent of the substrate. On both substrates the STM image contrast in the submolecularly resolved images is dominated by the aromatic perylene system whereas the polar oxygen and nitrogen groups are invisible. The correlation of the observed inner structure of the molecules to their molecular structure allows us to compare our results with theoretical considerations.     

STM characterisation of organic molecules on H-terminated Si(111)

We present the first high resolution STM images of organic molecules on the technological important hydrogen terminated silicon surface. Ordered layers of PTCDA and PTCDI were prepared on this surface by organic molecular beam epitaxy. The submolecular contrast of these molecules on Si(111)/H obtained in the high resolution images agrees with the corresponding images on HOPG and MoS₂ substrates.     

Structural analysis of PTCDA monolayers on epitaxial graphene with ultra-high vacuum scanning tunneling microscopy and high-resolution X-ray reflectivity

Epitaxial graphene, grown by thermal decomposition of the SiC (0001) surface, is a promising material for future applications due to its unique and superlative electronic properties. However, the innate chemical passivity of graphene presents challenges for integration with other materials for device applications. Here, we present structural characterization of epitaxial graphene functionalized by the organic semiconductor perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA). A combination of ultra-high vacuum scanning tunneling microscopy (STM) and high-resolution X-ray reflectivity (XRR) is used to extract lateral and vertical structures of 0, 1, and 2 monolayer (ML) PTCDA on epitaxial graphene. Both Fienup-based phase-retrieval algorithms and model-based least-squares analyses of the XRR data are used to extract an electron density profile that is interpreted in terms of a stacking sequence of molecular layers with specific interlayer spacings. Features in the STM and XRR analysis indicate long-range molecular ordering and weak π–π* interactions binding PTCDA molecules to the graphene surface. The high degree of both lateral and vertical ordering of the self-assembled film demonstrates PTCDA functionalization as a viable route for templating graphene for the growth and deposition of additional materials required for next-generation electronics and sensors.     

Bias-dependent STM images of oxygen-induced structures on Ti(0001) facets

Titanium films grown on Si(111) surfaces in ultrahigh vacuum were investigated using scanning tunneling microscopy (STM). STM images of adsorbate structures induced by oxygen adsorption on Ti(0001) facets are observed to change from protrusions to depressions depending on the applied bias voltage. Using electron spectroscopic data we interpret our results in terms of local, oxygen-induced modifications of the density of states.     

Channel selective scanning tunneling spectroscopy

In this paper we simulate STM and STS experiments for CO monomers and dimers on Cu(1 1 1) surface. We show that the contrast of STM images can be attributed to interference effects between tunneling channels, and suggest that functionalizing the microscope tip improves the channel selectivity of STM. Furthermore, we show that voltage and position dependent tunneling spectra also reflect the same interference effects, but adds the energy resolution to the channel analysis. Especially in the case of nonresonant tunneling, STS measures local density of states only indirectly. The present study suggests that STS in constant height mode can be used in investigating the phase and energy sensitivity of tunneling channels in adsorbate molecules and nanostructures.     

Two-dimensional self-assembly of esters with different configurations at the liquid-solid interface

Self-assembled monolayers of hexadecyl palmitate (HP) and 3,3′-thiodipropionic acid di-n-octadecyl ester (TADE) physisorbed on highly oriented pyrolytic graphite (HOPG) are investigated using scanning tunneling microscope (STM) and computer simulation. Both molecules form alkane-like linear shapes to maximize the interactions with substrate when they adsorb on HOPG surface. The HP molecules self-assemble into lamellae with the chain-trough angle of 48°, which is the result of a shifting 3/2 units from the adjacent molecule in a lamella. Based on the simulation insights combined with STM images, we confirm that a perpendicular orientation appears in which the HP molecular backbone is rotated 90° with respect to the substrate such that the carbonyl points away from the HOPG surface. TADE molecules form three kinds of configurations with chain-trough angles of 90°, 72° and 60° by shifting 0, 1/2 and 1 units from their adjacent molecules, respectively. The bright stripes in STM images reveal the electron density distribution of the part between two ester groups. The energy differences of three TADE adsorption configurations by molecular mechanics (MM) simulation are used to explain the structural coexistence phenomenon. It is also shown that lattice match between alkyl chain of molecules and HOPG substrate could change molecular conformation upon self-assembly.     

Surface reactivity of oxygen on cleaved and sputtered graphite

The characterization of reactions which occur during the oxidation of highly oriented pyrolytic graphite (HOPG) was performed using high-resolution electron energy loss spectroscopy (HREELS) temperature programmed desorption (TPD), and scanning tunneling microscopy (STM). The results of this investigation provide spectroscopic evidence for the presence of semi-quinone functionalities on sputtered and oxidized HOPG STM images are presented to quantify the increase in defect sites after oxygen ion sputtering, and to correlate defect site density with reactivity.     

Scanning tunneling microscopy studies of diazo dye monolayers on HOPG

We report on scanning tunneling microscopy (STM) studies of monolayers of the diazo dye 4-[4-(N,N-dimethylamino)phenylazo]azobenzene (D2, summation formula C₂₀H₁₉N₅) on the basal plane of highly oriented pyrolytic graphite (HOPG). Monolayers of the dye were prepared by vapour deposition or by dissolving the molecules in the liquid crystal octylcyanobiphenyl (8CB). The STM images show a double-row structure exhibiting different types of lattice defects and various domains. High-resolution images allow the identification of individual molecules and the observation of intramolecular contrast. The different orientations of the rows can be explained by a commensurate registry of the molecules with the substrate. A model for the unit cell is proposed.     

Insight into STM image contrast of n-tetradecane and n-hexadecane molecules on highly oriented pyrolytic graphite

Two-dimensional ordered patterns of n-tetradecane (n-C₁₄H₃₀) and n-hexadecane (n-C₁₆H₃₄) molecules at liquid/graphite interface have been directly imaged using scanning tunneling microscope (STM) under ambient conditions. STM images reveal that the two different kinds of molecules self-organize into ordered lamellar structures in which alkane chains of the molecules extend along one of three equivalent lattice axes of highly oriented pyrolytic graphite (HOPG) basal plane. For n-C₁₄H₃₀ molecules, the molecular axes are observed to tilt by 60° with respect to inter-lamellar trough lines and the carbon backbones of the alkane chains are perpendicular to the HOPG basal plane in an all-trans conformation. However, for n-C₁₆H₃₄ molecules, the molecular axes are perpendicular to lamellar borders (90°) and the planes of the all-trans carbon skeletons are parallel to the graphite basal plane. The results clearly indicate that outmost hydrogen atoms of the alkane chains dominate atom-scaled features of the STM images. That is, in the case of long-chain alkane molecules, topographic effects dominantly determine STM image contrast of the methylene regions of the alkane chains that are adsorbed on HOPG.     

STM simulation of molecules on ultrathin insulating overlayers using tight-binding: Au-pentacene on NaCl bilayer on Cu

We present fast and efficient tight-binding (TB) methods 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, STM can be used to image the frontier molecular orbitals of the adsorbate. These images can be simulated with a very efficient scheme based on hopping integrals 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 methods are found to be consistent with both DFT calculations and experimental data.     

Adsorption geometry of PTCDA on 2H-NbSe2

Low-temperature scanning tunnelling microscopy of submonolayers of PTCDA adsorbed on 2H-NbSe₂ reveals an adsorbate layer that is neither commensurate with the substrate lattice nor with the charge density wave periodicity. The observed smallness of deviations from the PTCDA bulk-state unit-cell dimensions indicates that PTCDA film formation is dominated by intermolecular interactions rather than by interaction between PTCDA and 2H-NbSe₂. PACS 61.66.Hq; 68.35.Bs; 68.37.Ef; 68.43.Fg     

Substrate-interaction,long-range order,and epitaxy of large organic adsorbates

Large and symmetric organic molecules (>200 amu) can form highly-ordered adsorbate layers and thin films when they are deposited by vacuum sublimation on clean reactive surfaces. In such cases covalent bonding often occurs via the molecular -system leading to a parallel orientation of the adsorbate as shown for oligothiophenes and PTCDA on Ag(1 1 1). A proper choice of the substrate and/or a preadsorbate may also cause an upright orientation with bonding via a reactive group of the molecule (example: NDCA/Ni(1 11)). Most of the used molecules yield long-range ordered monolayers with large, almost defect-free domains. The stronger the bonding and the smaller the molecule the more likely is the formation of commensurate superstructures which indicate site-specific adsorption even for such large molecules as PTCDA or EC4T. Organic epitaxy is discussed and shown for a particular system, PTCDA on Ag(1 1 1), for which the structure of the monolayer is nearly identical to that of the-modification of PTCDA crystals, whereas on other substrates (e.g. Si(1 1 1), Ge(1 0 0)) a disordered interface and hence no true epitaxy is found.     

Study of scanning tunneling microscopy images and probable relaxations of the SrTiO3(100) surface by electronic structure calculations

Partial electron density plots were calculated for a model SrTiO₃(100) surface with √5 × √5 ordered oxygen vacancy to examine why the bright spots of the scanning tunneling microscopy (STM) images of SrTiO₃(100) observed in ultrahigh vacuum (UHV) correspond to the oxygen vacancy sites. Possible dependence of the image on the polarity and magnitude of the bias voltage was also discussed on the basis of partial electron density plot calculations. Our study strongly suggests that the UHV STM imaging involves the lowest-lying d-block level of every two Ti³⁺ centers adjacent to an oxygen vacancy, the tip-sample distance involved in the UHV STM experiments is substantially larger than that involved in typical ambient-condition STM imaging, and the Ti⁴⁺ and Ti³⁺ sites of SrTiO₃(100) are reconstructed.     

ATOMIC CHARGE SUPERPOSITION CALCULATIONS OF STM IMAGES OF 2D-ORDERED AMINO ACID ADSORBATES(Ⅱ)

In the preceding paper, we have successfully used the atomic charge superposition (ACS) method to calculate STM images of 2D-ordered structures of glycine molecules adsorbed on graphite (HOPG). In this work we focus on alanine/HOPG system. Firstly, we make a thorough searching for all of the possible 2D-ordered aggregation structures that can form linear chains or 2D nets of hydrogen bonds between the molecules and simultaneously satisfy the Van der Waal's radii of the condtituent atoms, just like in the case of 3D crystal of the molecules. Secondly, in order to interpret the experimental images, we use the ACS method to calculate STM images of the possible structures. It turns out that many of the experimental images can be interpreted satisfactorily with their calculated counterparts. This result further exhibits the great potential of using STM to study organic and biological molecules.     

Interplay between metal-free phthalocyanine molecules and Au(110) substrates

Metal-free phthalocyanine (Pc) molecules adsorbed on the Au(110) surface have been studied both experimentally (STM, LEED) and with density functional calculations. A strong interaction between substrate and adsorbate is observed. On the one hand, a clear template effect of the anisotropic substrate is observed: already at low coverages, the Pc molecules adsorb in various typical row patterns. On the other hand, the molecular adsorption modifies the substrate: at coverages higher than 0.25 monolayers, the usual (1 × 2) reconstruction is converted to a (1 × 3) reconstruction. First principle DFT calculations yield adsorption geometries that agree with the measured STM images and adsorption energies in the range of 2–3 eV. The adsorption leads to covalent and van der Waals interactions between adsorbate and substrate and is accompanied by a considerable charge transfer.     

Barrier height imaging of Si(1 1 1)3 × 1-Ag reconstructed surfaces

We investigated the bias voltage polarity dependence of atomically resolved barrier height (BH) images on Si(1 1 1)3 × 1-Ag surfaces. The BH images were very similar to scanning tunneling microscopy (STM) images in both the empty and filled states. This similarity strongly supports the interpretation that the BH image reflects the vertical decay rate of the surface local density of states (LDOS). Differences in contrast and protrusion shapes between BH and STM images were observed. We attributed these differences to the geometric contribution to the STM image and to the improved spatial resolution of the BH image due to the lock-in technique.     

ATOMIC CHARGE SUPERPOSITION CALCULATIONS OF STM IMAGES OF 2D-ORDERED AMINO ACID ADSORBATES(Ⅰ)

In a previous STM investigation by Yang and co-workers a variety of 2D ordered atomic-scale features of glycine molecules adsorbed on graphite were observed and several models have been proposed to interpret these features. In the present work, atomic charge superposition(ACS) calculations of STM images of their models were carried out. The calculated images match the experimental ones fairly well, indicating the general validity of the ACS method to the glycine/graphite system and the correctness of their interpretations. The reason of the validity, the origin of the atomic resolution, and the proper tip-sample distance are also discussed.     

ATOMIC CHARGE SUPERPOSITION CALCULATIONS OF STM IMAGES OF 2D-ORDERED AMINO ACID ADSORBATES(Ⅰ)

In a previous STM investigation by Yang and co-workers a variety of 2D ordered atomic-scale features of glycine molecules adsorbed on graphite were observed and several models have been proposed to interpret these features. In the present work, atomic charge superposition(ACS) calculations of STM images of their models were carried out. The calculated images match the experimental ones fairly well, indicating the general validity of the ACS method to the glycine/graphite system and the correctness of their interpretations. The reason of the validity, the origin of the atomic resolution, and the proper tip-sample distance are also discussed.