Probing the conformation of physisorbed molecules at the atomic scale using STM manipulation

Orientation transitions and chiral assemblies of para-terphenyl molecules on Cd(0001)

The interplay between orientation transition and chiral self-assemblies of para-terphenyl (P3P) molecules on the Cd(0001) surface has been investigated using low temperature scanning tunneling microscopy and density functional theory calculations. Three distinct molecular orientations have been discerned from the self-assembled thin films of P3P. At the low coverage, flat-lying molecules appear in the homochiral domains with the incommensurate registry to the substrate. With the coverage increasing, the incoming molecules are incorporated into the first layer with edge-on orientation and form the self-assembled zigzag chains. The alternative arrangement of zigzag chains with opposite chirality leads to the formation of a c(4 × 2) superstructure, in which the tilted molecules exhibit orientational frustration and fuzzy noises. The analysis of the tunneling spectra reveals that the electronic structure of P3P layers is contingent upon the hybridization between the electronic states of P3P molecules and the Cd(0001) surface. These results provide important insights into the interplay between orientational transition and chiral assembly of P3P molecules on metal substrates.

One-Dimensional Lateral Force Anisotropy at the Atomic Scale in Sliding Single Molecules on a Surface

Using a q+ atomic force microscopy at low temperature, a sexiphenyl molecule is slid across an atomically flat Ag(111) surface along the direction parallel to its molecular axis and sideways to the axis. Despite identical contact area and underlying surface geometry, the lateral force required to move the molecule in the direction parallel to its molecular axis is found to be about half of that required to move it sideways. The origin of the lateral force anisotropy observed here is traced to the one-dimensional shape of the molecule, which is further confirmed by molecular dynamics simulations. We also demonstrate that scanning tunneling microscopy can be used to determine the comparative lateral force qualitatively. The observed one-dimensional lateral force anisotropy may have important implications in atomic scale frictional phenomena on materials surfaces.

Imaging Charge Localization in a Conjugated Oligophenylene

Polaron formation in conjugated polymers has a major impact on their optical and electronic properties. In polyphenylene, the molecular conformation is determined by a delicate interplay between electron delocalization and steric effects. Injection of excess charges is expected to increase the degree of conjugation, leading to structural distortions of the chain. Here we investigated at the single-molecule level the role of an excess charge in an individual oligophenylene deposited on sodium chloride films. By combining sub-molecular-resolved atomic force microscopy with redox-state-selective orbital imaging, we characterize both structural and electronical changes occurring upon hole injection. While the neutral molecule exhibits a delocalized frontier orbital, for the cationic radical the excess charge is observed to localize, inducing a partial planarization of the molecule. These results provide direct evidence for self-trapping of the excess charge in oligophenylenes, shedding light on the interplay of charge localization and structural distortion.

Absence of Nonlocal Manipulation of Oxygen Atoms Inserted below the Si(111)-7×7 Surface

The injection of electrons from the scanning tunneling microscope tip can be used to perform nanoscale chemistry and study hot electron transport through surfaces. While nonlocal manipulation has been demonstrated primarily for aromatic adsorbates, here we confirm that oxygen atoms bonded to the Si(111) surface can also be nonlocally manipulated, and we fit the measured manipulation data to a single channel decay model. Unlike aromatic adsorption systems, oxygen atoms also insert below the surface of silicon. Although the inserted oxygen can be manipulated when the tip is directly over the relevant silicon adatom, it is not possible to induce nonlocal manipulation of inserted oxygen atoms at the same bias. We attribute this to the electrons injected at +4 eV initially relaxing to couple to the highest available surface state at +3.4 eV before laterally transporting through the surface. With a manipulation threshold of 3.8 eV for oxygen inserted into silicon, once carriers have undergone lateral transport, they do not possess enough energy to manipulate and remove oxygen atoms inserted beneath the surface of silicon. This result confirms that nonlocal nanoscale chemistry using the scanning tunneling microscope tip is dependent not only on the energy required for atomic manipulation, but also on the energy of the available surface states to carry the electrons to the manipulation site.

Comparing the Self-Assembly of Sexiphenyl-Dicarbonitrile on Graphite and Graphene on Cu(111)

A comparative study on the self-assembly of sexiphenyl-dicarbonitrile on highly oriented pyrolytic graphite and single-layer graphene on Cu(111) is presented. Despite an overall low molecule-substrate interaction, the close-packed structures exhibit a peculiar shift repeating every four to five molecules. This shift has hitherto not been reported for similar systems and is hence a unique feature induced by the graphitic substrates.

Polymorphic self-assembly of pyrazine-based tectons at the solution-solid interface

Exploring the surface self-assembly of small molecules that act as building blocks (tectons) for complex supramolecular structures is crucial for realizing surface-supported functional molecular devices. Here, we report on the synthesis and surface self-assembly of a new pyrazine-derived molecule with pyridine pendants. Ambient scanning tunneling microscopy investigation at the solution-solid interface reveals polymorphic self-assembly of these molecules on a HOPG substrate. Two different molecular packing structures with equal distribution are observed. Detailed analysis of the STM images emphasizes the crucial role of weak intermolecular hydrogen bonding, and molecule-substrate interactions in the formation of the observed polymorphs. Such weak hydrogen bonding interactions are highly desirable for the formation of modular supramolecular architectures since they can provide sufficiently robust molecular structures and also facilitate error correction.

Energy level alignment at organic/inorganic semiconductor heterojunctions: Fermi level pinning at the molecular interlayer with a reduced energy gap

A lying (L) molecular interlayer between ZnO and standing (S) sexiphenyl molecules leads to “concealed” Fermi level pinning.

On-Surface Formation of Cumulene by Dehalogenative Homocoupling of Alkenyl gem-Dibromides

The on-surface activation of carbon-halogen groups is an efficient route to produce radicals for constructing various hydrocarbons and carbon nanostructures. To date, the employed halide precursors have only one halogen attached to a carbon atom. It is thus of interest to study the effect of attaching more than one halogen atom to a carbon atom with the aim of producing multiple unpaired electrons. By introducing an alkenyl gem-dibromide, cumulene products were fabricated on a Au(111) surface by dehalogenative homocoupling reactions. The reaction products and pathways were unambiguously characterized by a combination of high-resolution scanning tunneling microscopy and non-contact atomic force microscopy measurements together with density functional calculations. This study further supplements the database of on-surface synthesis strategies and provides a facile manner for incorporation of more complicated carbon scaffolds into surface nanostructures.

Correlation Effects in Scanning Tunneling Microscopy Images of Molecules Revealed by Quantum Monte Carlo

Scanning tunneling microscopy (STM) and spectroscopy probe the local density of states of single molecules electrically insulated from the substrate. The experimental images, although usually interpreted in terms of single-particle molecular orbitals, are associated with quasiparticle wave functions dressed by the whole electron-electron interaction. Here we propose an ab initio approach based on quantum Monte Carlo to calculate the quasiparticle wave functions of molecules. Through the comparison between Monte Carlo wave functions and their uncorrelated Hartree-Fock counterparts we visualize the electronic correlation embedded in the simulated STM images, highlighting the many-body features that might be observed.

Manipulation resolves non-trivial structure of corrole monolayer on Ag(111)

Non-trivial arrangement of molecules within a molecular network complicates structure determination due to interdigitation, partial overlap, or stacking. We demonstrate that combined imaging and lateral manipulation with a scanning tunneling microscope resolves the intricate structure of a molecular network in two-dimensions in a straightforward manner. The network, formed by a monolayer of 5,10,15-tris(pentafluorophenyl)-corrole molecules on Ag(111), is manipulated for the first time with single-molecule precision. Our results reveal a shingle-like packing of partially overlapping corrole molecules. Density functional theory calculations support our findings.

Atom-by-atom assembly

Atomic manipulation using a scanning tunneling microscope (STM) tip enables the construction of quantum structures on an atom-by-atom basis, as well as the investigation of the electronic and dynamical properties of individual atoms on a one-atom-at-a-time basis. An STM is not only an instrument that is used to 'see' individual atoms by means of imaging, but is also a tool that is used to 'touch' and 'take' the atoms, or to 'hear' their movements. Therefore, the STM can be considered as the 'eyes', 'hands' and 'ears' of the scientists, connecting our macroscopic world to the exciting atomic world. In this article, various STM atom manipulation schemes and their example applications are described. The future directions of atomic level assembly on surfaces using scanning probe tips are also discussed.

Hydrogen nanobubble at normal hydrogen electrode

Electrochemically formed hydrogen nanobubbles at a platinum rotating disk electrode (RDE) were detected by re-oxidation charge. The dissolution time course of the hydrogen nanobubbles was measured by AFM tapping topography under open-circuit conditions at stationary platinum and gold single-crystal electrodes. The bubble dissolution at platinum was much faster than that at gold because two types of diffusion, bulk and surface diffusion, proceeded at the platinum surface, whereas surface diffusion was prohibited at the gold electrode. These findings indicated that the electrochemical reaction of normal hydrogen electrode partly proceeded heterogeneously on the three-phase boundary around the hydrogen nanobubble.

Local Ionization Dynamics Traced by Photoassisted Scanning Tunneling Microscopy: A Theoretical Approach

For tracing the spatiotemporal evolution of electronic systems, we suggest and analyze theoretically a setup that exploits the excellent spatial resolution based on scanning tunneling microscopy techniques combined with the temporal resolution of femtosecond pump-probe photoelectron spectroscopy. As an example, we consider the laser-induced, local vibrational dynamics of a surface-adsorbed molecule. The photoelectrons released by a laser pulse can be collected by the scanning tip and utilized to access the spatiotemporal dynamics. Our proof-of-principle calculations are based on the solution of the time-dependent Schrödinger equation supported by the ab initio computation of the matrix elements determining the dynamics.

High-quality 2D metal-organic coordination network providing giant cavities within mesoscale domains

A surface-supported open metal-organic nanomesh featuring a 24 nm(2) cavity size and extending to mum domains was fabricated by Co-directed assembly of para-hexaphenyl-dicarbonitrile linker molecules in two dimensions. The metallosupramolecular lattice is thermally robust and resides fully commensurate on the employed Ag(111) substrate as directly verified by high-resolution scanning tunneling microscopy observations.

Charge transfer in the TCNQ-sexithiophene complex

Molecular crystals from thiophene molecules can be doped with TCNQ-F4 molecules for use in all-organic optoelectronic and semiconductor devices. The charge transfer and the molecular orbital energy level formation in between these two organic molecules are investigated here by density functional theory calculations. The isolated molecules are calculated nonbonded and bonded together, forming a charge transfer complex (CTC). The relaxed structure of the complex shows essentially coplanar and centered molecules with the alpha-sexithiophene rings tilted alternatingly by 4.8 degrees. The bond formation of these molecules results in a charge transfer of approximately 0.4 e from the alpha-sexithiophene to the TCNQ-F4 molecule. The highest occupied molecular orbital-lowest unoccupied molecular orbital gap width is reduced as compared to the isolated molecules due to the newly formed orbitals in the CTC. Upon adsorption on a Au(111) surface, electrons are transferred onto the molecule complex, thereby causing the molecular levels to align asymmetric with respect to the charge neutrality level. The theoretical results for the single molecule and CTC layer are compared to experimental photoemission and scanning tunneling spectroscopy results.

Adsorption, manipulation and self-assembling of TBrPP-Co molecules on a Ag/Si(111) surface by scanning tunnelling microscopy

Individual adsorption and two-dimensional assembling of 5,10,15,20-tetrakis-(4-bromophenyl)-porphyrin-Co (TBrPP-Co) molecules on a Si(111)-[Formula: see text] Ag reconstructed surface have been studied using low-temperature scanning tunnelling microscopy (STM). All the isolated molecules are observed in a planar shape with slight distortion. The isolated molecules can be controllably rotated with an STM tip to the orientation along the trigonal lattice ([Formula: see text] direction) of the substrate. With an increased coverage (0.07 ML) and appropriate annealing, the molecules assemble to form three types of ordered phase. The long-range ordered structures, however, disappear at higher coverage (0.75 ML).

"Soft" metallic contact to isolated C60 molecules

C60 adsorbed on a monolayer of hexaazatriphenylene-hexanitrile (HATCN) on Ag(111) is investigated by ultraviolet photoelectron spectroscopy (UPS) and scanning tunneling microscopy. UPS and quantum-mechanical modeling show that HATCN chemisorbed on Ag(111) displays metallic character. This metallic molecular layer decouples C60 electronically from the Ag substrate and simultaneously acts both as template for the stable adsorption of isolated C60 molecules at room temperature and as "soft" metallic contact for subsequently deposited molecules.

Chiral kagomé lattice from simple ditopic molecular bricks

Self-assembly techniques allow for the fabrication of highly organized architectures with atomic-level precision. Here, we report on molecular-level scanning tunneling microscopy observations demonstrating the supramolecular engineering of complex, regular, and long-range ordered periodic networks on a surface atomic lattice using simple linear molecular bricks. The length variation of the employed de novo synthesized linear dicarbonitrile polyphenyl molecules translates to distinct changes of the bonding motifs that lead to hierarchic order phenomena and unexpected changes of the surface tessellations. The achieved 2D organic networks range from a close-packed chevron pattern via a rhombic network to a hitherto unobserved supramolecular chiral kagomé lattice.

Organic Molecular Beam Deposition of Oligophenyls on Au(111): A Study by X-ray Absorption Spectroscopy

Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy has been applied to reveal the molecular arrangement of ultrathin oligophenyl films [p-quaterphenyl (4P) and p-hexaphenyl (6P)] on Au(111). In the half-monolayer films the molecules lie flat on the surface but still have a considerable inter-ring twist of 30 degrees -40 degrees , similar to the gas-phase conformation. In the saturated monolayer film the second half of the molecules is side-tilted by an angle of less than 66 degrees with respect to the surface. This arrangement is already similar to that in bulk net planes of thicker films parallel to the surface, that is, the 4P(211) and 6P(21-3) planes, respectively.

Nanoassembly of a Fractal Polymer: A Molecular "Sierpinski Hexagonal Gasket"

Mathematics and art converge in the fractal forms that also abound in nature. We used molecular self-assembly to create a synthetic, nanometer-scale, Sierpinski hexagonal gasket. This nondendritic, perfectly self-similar fractal macromolecule is composed of bis-terpyridine building blocks that are bound together by coordination to 36 Ru and 6 Fe ions to form a nearly planar array of increasingly larger hexagons around a hollow center.