The construction of metal–organic molecular wires is important for the design of specific functional devices but has been a great challenge for experimental technology. Here we report the formation of one-dimensional metal–organic structures by direct deposition of pentacene molecules on the Au(110) surface with subsequent thermal annealing. These metal–organic molecular wires were systematically explored by scanning tunneling microscopy (STM) and density functional theory calculations. At submonolayer coverage, during annealing at ∼470 K, the adsorbed molecules induce both Au(110)-(1 × 3) surface reconstruction, where two atomic rows are missing every three rows on the Au(110) surface, with the end-to-end pentacene configuration and Au(110)-(1 × 6) surface reconstruction, where five rows are missing every six rows on the surface, with the side-by-side configuration. Further annealing at ∼520 K results in Au-adatom-coordinated metal–organic molecular wires with a new side-by-side configuration of pentacene molecules on the Au(110)-(1 × 6) surface. The Au adatoms linking neighboring pentacene molecules, indicated by bright features in the STM image, were strongly evidenced by the STM simulations. Therefore, metal–organic molecular wires of pentacene on Au(110) were achieved through coordination bonds between native Au atoms and the −CH– groups of pentacene molecules.

We demonstrate cascade manipulation between magic number gold–fullerene hybrid clusters by channelling thermal energy into a specific reaction pathway with a trigger from the tip of a scanning tunnelling microscope (STM). The (C60)m–Aun clusters, formed via self-assembly on the Au(111) surface, consist of n Au atoms and m C60 molecules; the three smallest stable clusters are (C60)7–Au19, (C60)10–Au35, and (C60)12–Au49. The manipulation cascade was initiated by driving the STM tip into the cluster followed by tip retraction. Temporary, partial fragmentation of the cluster was followed by reorganization. Self-selection of the correct numbers of Au atoms and C60 molecules led to the formation of the next magic number cluster. This cascade manipulation is efficient and facile with an extremely high selectivity. It offers a way to perform on-surface tailoring of atomic and molecular clusters by harnessing thermal energy, which is known as the principal enemy of the quest to achieve ultimate structural control with the STM.Keywords: atom manipulation; Cluster; fullerene; nanostructures; scanning tunneling microscopy; self-assembly;

Silicon-based two-dimensional (2D) materials are uniquely suited for integration in Si-based electronics. Silicene, an analogue of graphene, was recently fabricated on several substrates and was used to make a field-effect transistor. Here, we report that when Ru(0001) is used as a substrate, a range of distinct monolayer silicon structures forms, evolving toward silicene with increasing Si coverage. Low Si coverage produces a herringbone structure, a hitherto undiscovered 2D phase of silicon. With increasing Si coverage, herringbone elbows evolve into silicene-like honeycomb stripes under tension, resulting in a herringbone-honeycomb 2D superlattice. At even higher coverage, the honeycomb stripes widen and merge coherently to form silicene in registry with the substrate. Scanning tunneling microscopy (STM) was used to image the structures. The structural stability and electronic properties of the Si 2D structures, the interaction between the Si 2D structures and the Ru substrate, and the evolution of the distinct monolayer Si structures were elucidated by density functional theory (DFT) calculations. This work paves the way for further investigations of monolayer Si structures, the corresponding growth mechanisms, and possible functionalization by impurities.

Using atomic bromine and 2,6-diphenylanthracene (DPA), we successfully constructed and characterized the large-area 2D chiral networks on Ag(111) and Cu(111) surfaces by combining molecular beam epitaxy with scanning tunneling microscopy. The Br atoms distribute themselves periodically in the network with the maximum number of −C–H···Br hydrogen bonds. Density functional theory calculations demonstrate that the hydrogen bonds contribute to the stability of the Br-organic networks. In addition, by controlling the ratio of bromine atoms to DPA molecules, different patterns of Br-organic networks were obtained on Ag(111) surfaces. Further experiments with 2,6-di(4-cyclohexylphenyl)anthracene on Ag(111) produced analogous atomic bromine guided 2D chiral networks.

Recently, single-layer transition-metal dichalcogenides have drawn significant attention due to their remarkable physical properties in the monolayer as well as at the edges. Here, we constructed high-quality, single-layer MoSe2 islands on the Au(111) surfaces in ultrahigh vacuum by molecular beam epitaxy. All of the islands have hexagonal or triangular shapes with two kinds of well-defined edges. Scanning tunneling spectroscopy (STS) curves show notable differences in positive sample bias for the two types of edges. Density functional theory calculations for several edge configurations of MoSe2 confirm that the STS differences are attributed to the coupling between the pz orbital of Se atoms and the dxz orbital of Mo atoms, and the two types of observed edge terminations are the bare Se edge and selenium-saturated Mo edge.Keywords: density functional theory; edge terminations; molecular beam epitaxy; scanning tunneling microscopy; scanning tunneling spectroscopy; single-layer MoSe2 islands;

We predict theoretical existence of intrinsic two-dimensional organic topological insulator (OTI) states in Cu–dicyanoanthracene (DCA) lattice, a system that has also been grown experimentally on Cu substrate, based on first-principle density functional theory calculations. The pz-orbital Kagome bands having a Dirac point lying exactly at the Fermi level are found in the freestanding Cu–DCA lattice. The tight-binding model analysis, the calculated Chern numbers, and the semi-infinite Dirac edge states within the spin–orbit coupling gaps all confirm its intrinsic topological properties. The intrinsic TI states are found to originate from a proper number of electrons filling of the hybridized bands from Cu atomic and DCA molecular orbitals based on which similar lattices containing noble metal atoms (Au and Cu) and those molecules with two CN groups (DCA and cyanogens) are all predicted to be intrinsic OTIs.

Single-layer transition-metal dichalcogenides (TMDs) receive significant attention due to their intriguing physical properties for both fundamental research and potential applications in electronics, optoelectronics, spintronics, catalysis, and so on. Here, we demonstrate the epitaxial growth of high-quality single-crystal, monolayer platinum diselenide (PtSe2), a new member of the layered TMDs family, by a single step of direct selenization of a Pt(111) substrate. A combination of atomic-resolution experimental characterizations and first-principle theoretic calculations reveals the atomic structure of the monolayer PtSe2/Pt(111). Angle-resolved photoemission spectroscopy measurements confirm for the first time the semiconducting electronic structure of monolayer PtSe2 (in contrast to its semimetallic bulk counterpart). The photocatalytic activity of monolayer PtSe2 film is evaluated by a methylene-blue photodegradation experiment, demonstrating its practical application as a promising photocatalyst. Moreover, circular polarization calculations predict that monolayer PtSe2 has also potential applications in valleytronics.

Doping graphene with boron has been difficult because of high reaction barriers. Here, we describe a low-energy reaction route derived from first-principles calculations and validated by experiments. We find that a boron atom on graphene on a ruthenium(0001) substrate can replace a carbon by pushing it through, with substrate attraction helping to reduce the barrier to only 0.1 eV, implying that the doping can take place at room temperature. High-quality graphene is grown on a Ru(0001) surface and exposed to B2H6. Scanning tunneling microscopy/spectroscopy and X-ray photoelectron spectroscopy confirmed that boron is indeed incorporated substitutionally without disturbing the graphene lattice.

Structural and mechanical properties of self-assembled metal-free naphthalocyanine (H2Nc) films on a Ag(111) surface are studied. Six self-assembled domains are observed by scanning tunneling microscopy (STM). Combining the high-resolution STM images and density functional theory (DFT) based calculations, we found that molecules adsorbed flatly on the substrate by forming six different interlocked square-like unit cells with different lattice parameters. DFT calculations indicated comparable adsorption energies for all the configurations. Six domains with different lattice parameters present different strain states, giving us a possibility to evaluate the Young’s modulus of the metal-free naphthalocyanine films on the Ag(111) surface. We found that the Young’s modulus of H2Nc is comparable to those of typical conjugated organic-molecule-based crystals (e.g., naphthalene), providing useful information for future applications when the elastic properties should be concerned.

The Pb intercalation at the interface of monolayer graphene (MG) and Ru(0001) is studied by means of low temperature scanning tunneling microscopy (LT-STM) and Raman spectroscopy. Despite being covered by MG, the atomic structures of the Pb layer formed between MG and Ru(0001) have been directly imaged using LT-STM. The Pb layer intercalated underneath MG exhibits a √7 × √7-R19° superstructure with respect to the Ru(0001) surface. STM and Raman spectroscopy measurements and density functional theory calculations reveal that the epitaxial MG are effectively decoupled from the Ru(0001) substrate and recover its intrinsic electronic property after Pb intercalation.

We predict a family of 2D carbon (C) allotropes, square graphynes (S-graphynes) that exhibit highly anisotropic Dirac fermions, using first-principle calculations within density functional theory. They have a square unit-cell containing two sizes of square C rings. The equal-energy contour of their 3D band structure shows a crescent shape, and the Dirac crescent has varying Fermi velocities from 0.6 × 105 to 7.2 × 105 m/s along different k directions. Near the Fermi level, the Dirac crescent can be nicely expressed by an extended 2D Dirac model Hamiltonian. Furthermore, tight-binding band fitting reveals that the Dirac crescent originates from the next-nearest-neighbor interactions between C atoms. S-graphynes may be used to build new 2D electronic devices taking advantages of their highly directional charge transport.

Cyclotrimerization of alkynes to aromatics represents a promising approach to two-dimensional conjugated networks due to its single-reactant and atom-economy attributes, in comparison with other multicomponent coupling reactions. However, the reaction mechanism of alkyne cyclotrimerization has not yet been well understood due to characterization challenges. In this work, we take a surface reaction approach to study fundamental polymerization mechanism by using a diyne monomer named 4,4′-diethynyl-1,1′-biphenyl as a test bed. We have succeeded in directly characterizing reactants, intermediates, and their reaction products with the aid of scanning tunneling microscope, which allows us to gain mechanistic insights into the reaction pathways. By combining with density functional theory calculation, our result has revealed for the first time that the polycyclotrimerization is a two-step [2+2+2] cyclization reaction. This work provides an in-depth understanding of polycyclotrimerization process at the atomic level, offering a new avenue to design and construct of single-atom-thick conjugated networks.

Silicene, a two-dimensional (2D) honeycomb structure similar to graphene, has been successfully fabricated on an Ir(111) substrate. It is characterized as a (√7×√7) superstructure with respect to the substrate lattice, as revealed by low energy electron diffraction and scanning tunneling microscopy. Such a superstructure coincides with the (√3×√3) superlattice of silicene. First-principles calculations confirm that this is a (√3×√3)silicene/(√7×√7)Ir(111) configuration and that it has a buckled conformation. Importantly, the calculated electron localization function shows that the silicon adlayer on the Ir(111) substrate has 2D continuity. This work provides a method to fabricate high-quality silicene and an explanation for the formation of the buckled silicene sheet.

The template-directed assembly of planar pentacene molecules on epitaxial graphene grown on Ru(0001) (G/Ru) has been investigated by means of low-temperature scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. STM experiments find that pentacene adopts a highly selective and dispersed growth mode in the initial stage. By using DFT calculations including van der Waals interactions, we find that the configuration with pentacene adsorbed on face-centered cubic (fcc) regions of G/Ru is the most stable one, which accounts for the selective adsorption at low coverage. Moreover, at high coverage, we have successfully controlled the molecular assembly from amorphous, local ordering, to long-range order by optimizing the deposition rate and substrate temperature.

A key requirement for the future applicability of molecular electronics devices is a resilience of their properties to mechanical deformation. At present, however, there is no fundamental understanding of the origins of mechanical properties of molecular films. Here we use quinacridone, which possesses flexible carbon side chains, as a model molecular system to address this issue. Eight molecular configurations with different molecular coverage are identified by scanning tunneling microscopy. Theoretical calculations reveal quantitatively the roles of different molecule–molecule and molecule–substrate interactions and predict the observed sequence of configurations. Remarkably, we find that a single Young’s modulus applies for all configurations, the magnitude of which is controlled by side chain length, suggesting a versatile avenue for tuning not only the physical and chemical properties of molecular films but also their elastic properties.

Using first-principles calculations based on density functional theory, we studied the possible geometric configurations and electronic structures of three types of monolayer boron sheets (BSs) on different metal (Mg, Al, Ti, Au, and Ag) surfaces. We find that, when adsorbed on metal surfaces, hexagonal BS (h-BS) is more energy-favorable than triangular BS or mixed hexagonal-triangular BS, and the atop-site adsorption configuration is the most favored. For all h-BS/metal configurations, electrons are observed to transfer from metal to BS, due to the intrinsic electron deficiency of h-BS. Electronic structure analyses show that the substrates could be classified into two types according to the interactions between boron and metal: (1) h-BS on Mg(0001), Al(111), or Ti(0001) shows a relatively larger charge transfer and stronger BS–metal interactions, and the σ (in-plane) bands have the same profile as freestanding h-BS, except for a Fermi level shift caused by the charge transfer. (2) h-BS on Au(111) or Ag(111) surfaces has in-plane bands split into several subbands. A model of coronene on h-BS/Mg(0001) is also investigated, which shows that it is possible to decouple the molecular electronic structure from the metal surface by a buffer of a single sheet of boron.

Adsorption behavior of iron–phthalocyanine (FePc) at low submonolayer coverage on a reconstructed Au(111) single crystalline surface was investigated by a combination of low temperature scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. A site- and orientation-selective adsorption was found at different temperatures and molecular coverages by means of STM. Further DFT calculations demonstrate that the energy difference between different adsorption configurations leads to the selectivity, and thus the formation of one-dimensional molecular chains on the monatomic step edges in the fcc surface reconstruction domains. The exact adsorption site and configuration of the FePc molecule as well as the simulated STM images are obtained on the basis of DFT calculations, which is in good agreement with experimental observations.