Calculation of the benzene on rhodium STM images

Calculated and structural analyses of self-assembly formed by [7]thiaheterohelicene-2,13-carboxaldehyde molecules on Au(111)

Recently, the electronic and structural properties of large self-assembled domains of [7]thiaheterohelicene-2,13-carboxaldehyde helicene ([7]TH-dial) molecules on Au(111), Cu(001), and NiAl(110) metal surfaces have been characterized by scanning tunneling microscopy (STM). Several distinct areas of the self-assembled structures can be observed. To describe and explore the morphology of and the interactions in these distinct self-assembled nanostructures, we combine the results obtained through calculations in a semi-empirical framework and calculated STM images. It is revealed that these supramolecular nanostructures, on metallic substrates, originate from the two orientations P and M of the [7]TH-dial molecules linked in different orientations (head-to-tail, sideways, head-on, and tail-on) through van der Waals interactions. The results presented here provide valuable insights for understanding the intermolecular and substrate-molecule interactions within the self-assembled nanostructures of [7]TH-dial molecules on metallic surfaces.

Self-Assembly of Molecular Landers Equipped with Functional Moieties on the Surface: A Mini Review

The bottom-up fabrication of supramolecular and self-assembly on various substrates has become an extremely relevant goal to achieve prospects in the development of nanodevices for electronic circuitry or sensors. One of the branches of this field is the self-assembly of functional molecular components driven through non-covalent interactions on the surfaces, such as van der Waals (vdW) interactions, hydrogen bonding (HB), electrostatic interactions, etc., allowing the controlled design of nanostructures that can satisfy the requirements of nanoengineering concepts. In this context, non-covalent interactions present opportunities that have been previously explored in several molecular systems adsorbed on surfaces, primarily due to their highly directional nature which facilitates the formation of well-ordered structures. Herein, we review a series of research works by combining STM (scanning tunneling microscopy) with theoretical calculations, to reveal the processes used in the area of self-assembly driven by molecule Landers equipped with functional groups on the metallic surfaces. Combining these processes is necessary for researchers to advance the self-assembly of supramolecular architectures driven by multiple non-covalent interactions on solid surfaces.

A General Framework of Scanning Tunneling Microscopy Based on Bardeen's Approximation for Isolated Molecules

Scanning tunneling microscopy (STM) is one of the most popular techniques for precise characterization. Yet, its current theoretical implementation is often based on the periodic boundary condition with the Tersoff-Hamann approximation, which is inefficient to explore the tip states other than the s-wave and to treat properly the charged molecules that are ubiquitous in chemistry. In this work, we establish a general theoretical framework for STM image simulations, which is based on the Bardeen's approximation and utilizes the boundary condition of the cluster model. We develop an analytic algorithm for the precise evaluation of the transfer Hamiltonian matrix, addressing correctly the asymptotic behaviors of the tip states. Numerical results demonstrate that the molecular images under different STM tip states and mapping modes can be quantitatively simulated in the present framework, which paves the avenue for the conclusive investigation of the ground state electronic structures for either neutral or charged molecules.

Train of Single Molecule-Gears

Two molecule-gears, 1.2 nm in diameter with six teeth, are mounted each on a single copper adatom separated exactly by 1.9 nm on a lead surface using a low-temperature scanning tunneling microscope (LT-STM). A functioning train of two molecule-gears is constructed complete with a molecule-handle. Not mounted on a Cu adatom axle, this ancillary molecule-gear is mechanically engaged with the first molecule-gear of the train to stabilize its step-by-step rotation. Centered on its Cu adatom axle, the rotation of the first gear of the train step by step rotates the second similar to a train of macroscopic gears. From the handle to the first and to this second molecule-gear, the exact positioning of the two Cu adatom axles on the lead surface ensures that the molecular teeth-to-teeth mechanics is fully reversible.

Switching the Spin on a Ni Trimer within a Metal-Organic Motif by Controlling the On-Top Bromine Atom

Controlling the spin of metal atoms embedded in molecular systems is a key step toward the realization of molecular electronics and spintronics. Many efforts have been devoted to explore the influencing factors dictating the survival or quenching of a magnetic moment in a metal-organic molecule, and among others, the spin control by axial ligand attachments is the most promising. Herein, from the interplay of high-resolution scanning tunneling microscopy imaging/manipulation and scanning tunneling spectroscopy measurements together with density functional theory calculations, we successfully demonstrate that a Ni trimer within a metal-organic motif acquires a net spin promoted by the adsorption of an on-top Br atom. The spin localization in the trimetal centers bonded to Br was monitored via the Kondo effect. The removal of the Br ligand resulted in the switch from a Kondo ON to a Kondo OFF state. The magnetic state induced by the Br ligand is theoretically attributed to the enhanced Br 4p_z and Ni 3d_z² states due to the charge redistribution. The manipulation strategy reported here provides the possibility to explore potential applications of spin-tunable structures in spintronic devices.

Unraveling the molecular conformations of a single ruthenium complex adsorbed on the Ag(111) surface by calculations

The tris(dibenzoylmethanato)ruthenium (Ru(dbm)3) molecule has recently been characterized by scanning tunneling microscopy (STM) experiments upon adsorption on Ag(111). The adsorbed Ru(dbm)3 molecule shows two conformations with respect to the [11[combining macron]0] direction of the substrate, one with a three-lobed feature and the other one with a bi-lobed structure. For each of these structures, the molecule can take two geometries (states). Molecular mechanics calculations in a semi-empirical framework and STM calculated images reveal that these states on the substrate originate from the enantiomer of the Ru(dbm)3 molecule in the case of three-lobed structure and from the rotation of the two phenyls in the top dbm moities for the bi-lobed form.

Hydrogen interaction with graphene on Ir(1 1 1): a combined intercalation and functionalization study

We demonstrate a procedure for obtaining a H-intercalated graphene layer that is found to be chemically decoupled from the underlying metal substrate. Using high-resolution x-ray photoelectron spectroscopy and scanning tunneling microscopy techniques, we reveal that the hydrogen intercalated graphene is p-doped by about 0.28 eV, but also identify structures of interfacial hydrogen. Furthermore, we investigate the reactivity of the decoupled layer towards atomic hydrogen and vibrationally excited molecular hydrogen and compare these results to the case of non-intercalated graphene. We find distinct differences between the two. Finally, we discuss the possibility to form graphane clusters on an iridium substrate by combined intercalation and H atom exposure experiments.

Surface manipulation of a curved polycyclic aromatic hydrocarbon-based nano-vehicle molecule equipped with triptycene wheels

With a central curved chassis, a four-wheeled molecule-vehicle was deposited on a Au(111) surface and imaged at low temperature using a scanning tunneling microscope. The curved conformation of the chassis and the consequent moderate interactions of the four wheels with the surface were observed. The dI/dV constant current maps of the tunneling electronic resonances close to the Au(111) Fermi level were recorded to identify the potential energy entry port on the molecular skeleton to trigger and control the driving of the molecule. A lateral pushing mode of molecular manipulation and the consequent recording of the manipulation signals confirm how the wheels can step-by-step rotate while passing over the Au(111) surface native herringbone reconstructions. Switching a phenyl holding a wheel to the chassis was not observed for triggering a lateral molecular motion inelastically and without any mechanic push by the tip apex. This points out the necessity to encode the sequence of the required wheels action on the profile of the potential energy surface of the excited states to be able to drive a molecule-vehicle.

On-Surface Annulation Reaction Cascade for the Selective Synthesis of Diindenopyrene

We investigated the thermally induced on-surface cyclization of 4,10-bis(2'-bromo-4'-methylphenyl)-1,3-dimethylpyrene to form the previously unknown, nonalternant polyaromatic hydrocarbon diindeno[1,2,3-cd:1',2',3'-mn]pyrene on Au(111) using scanning tunneling microscopy and spectroscopy. The observed unimolecular reaction involves thermally induced debromination followed by selective ring closure to fuse the neighboring benzene moieties via a five-membered ring. The structure of the product has been verified experimentally as well as theoretically. Our results demonstrate that on-surface reactions give rise to unusual chemical reactivities and selectivities and provide access to nonalternant polyaromatic molecules.

Conformation Manipulation and Motion of a Double Paddle Molecule on an Au(111) Surface

The molecular conformation of a bisbinaphthyldurene (BBD) molecule is manipulated using a low-temperature ultrahigh-vacuum scanning tunneling microscope (LT-UHV STM) on an Au(111) surface. BBD has two binaphthyl groups at both ends connected to a central durene leading to anti/syn/flat conformers. In solution, dynamic nuclear magnetic resonance indicated the fast interexchange between the anti and syn conformers as confirmed by density functional theory calculations. After deposition in a submonolayer on an Au(111) surface, only the syn conformers were observed forming small islands of self-assembled syn dimers. The syn dimers can be separated into syn monomers by STM molecular manipulations. A flat conformer can also be prepared by using a peculiar mechanical unfolding of a syn monomer by STM manipulations. The experimental STM dI/dV and theoretical elastic scattering quantum chemistry maps of the low-lying tunneling resonances confirmed the flat conformer BBD molecule STM production. The key BBD electronic states for a step-by-step STM inelastic excitation lateral motion on the Au(111) are presented requiring no mechanical interactions between the STM tip apex and the BBD. On the BBD molecular board, selected STM tip apex positions for this inelastic tunneling excitation enable the flat BBD to move controllably on Au(111) by a step of 0.29 nm per bias voltage ramp.

Observation and modeling of conformational molecular structures driving the self-assembly of tri-adamantyl benzene on Ag(111)

A STM image of the hexagonal network of tri-adamantyl benzene molecules on Ag(111).

Supramolecular Rotor and Translator at Work: On-Surface Movement of Single Atoms

A supramolecular nanostructure composed of four 4-acetylbiphenyl molecules and self-assembled on Au (111) was loaded with single Au adatoms and studied by scanning tunneling microscopy at low temperature. By applying voltage pulses to the supramolecular structure, the loaded Au atoms can be rotated and translated in a controlled manner. The manipulation of the gold adatoms is driven neither by mechanical interaction nor by direct electronic excitation. At the electronic resonance and driven by the tunneling current intensity, the supramolecular nanostructure performs a small amount of work of about 8 × 10(-21) J, while transporting the single Au atom from one adsorption site to the next. Using the measured average excitation time necessary to induce the movement, we determine the mechanical motive power of the device, yielding about 3 × 10(-21) W.

Conductance of a single flexible molecular wire composed of alternating donor and acceptor units

Molecular-scale electronics is mainly concerned by understanding charge transport through individual molecules. A key issue here is the charge transport capability through a single--typically linear--molecule, characterized by the current decay with increasing length. To improve the conductance of individual polymers, molecular design often either involves the use of rigid ribbon/ladder-type structures, thereby sacrificing for flexibility of the molecular wire, or a zero band gap, typically associated with chemical instability. Here we show that a conjugated polymer composed of alternating donor and acceptor repeat units, synthesized directly by an on-surface polymerization, exhibits a very high conductance while maintaining both its flexible structure and a finite band gap. Importantly, electronic delocalization along the wire does not seem to be necessary as proven by spatial mapping of the electronic states along individual molecular wires. Our approach should facilitate the realization of flexible 'soft' molecular-scale circuitry, for example, on bendable substrates.

Real-space imaging of interfacial water with submolecular resolution

Water/solid interfaces are vital to our daily lives and are also a central theme across an incredibly wide range of scientific disciplines. Resolving the internal structure, that is, the O-H directionality, of water molecules adsorbed on solid surfaces has been one of the key issues of water science yet it remains challenging. Using a low-temperature scanning tunnelling microscope, we report submolecular-resolution imaging of individual water monomers and tetramers on NaCl(001) films supported by a Au(111) substrate at 5 K. The frontier molecular orbitals of adsorbed water were directly visualized, which allowed discrimination of the orientation of the monomers and the hydrogen-bond directionality of the tetramers in real space. Comparison with ab initio density functional theory calculations reveals that the ability to access the orbital structures of water stems from the electronic decoupling effect provided by the NaCl films and the precisely tunable tip-water coupling.

Observation and manipulation of hexa-adamantyl-hexa-benzocoronene molecules by low temperature scanning tunneling microscopy

Observation and manipulation of Ad₆HBC molecules by STM (image of a dimer created by molecular manipulation).

Mapping the first electronic resonances of a Cu phthalocyanine STM tunnel junction

Using a low temperature, ultrahigh vacuum scanning tunneling microscope (STM), dI/dV differential conductance maps were recorded at the tunneling resonance energies for a single Cu phthalocyanine molecule adsorbed on an Au(111) surface. We demonstrated that, contrary to the common assumption, such maps are not representative of the molecular orbital spatial expansion, but rather result from their complex superposition captured by the STM tip apex with a superposition weight which generally does not correspond to the native weight used in the standard Slater determinant basis set. Changes in the molecule conformation on the Au(111) surface further obscure the identification between dI/dV conductance maps and the native molecular orbital electronic probability distribution in space.

Mapping the excited states of single hexa-peri-benzocoronene oligomers

Electronic states of a molecule are usually analyzed via their decomposition in linear superposition of multielectronic Slater determinants built up from monoelectronics molecular orbitals. It is generally believed that a scanning tunneling microscope (STM) is able to map those molecular orbitals. Using a low-temperature ultrahigh vacuum (LT-UHV) STM, the dI/dV conductance maps of large single hexabenzocoronene (HBC) monomer, dimer, trimer, and tetramer molecules were recorded. We demonstrate that the attribution of a tunnel electronic resonance to a peculiar π molecular orbital of the molecule (or σ intermonomer chemical bond) in the STM junction is inappropriate. With an STM weak-measurement-like procedure, a dI/dV resonance results from the conductance contribution of many molecular states whose superposition makes it difficult to reconstruct an apparent molecular orbital electron probability density map.

Single molecule logical devices

After almost 40 years of development, molecular electronics has given birth to many exciting ideas that range from molecular wires to molecular qubit-based quantum computers. This chapter reviews our efforts to answer a simple question: how smart can a single molecule be? In our case a molecule able to perform a simple Boolean function is a child prodigy. Following the Aviram and Ratner approach, these molecules are inserted between several conducting electrodes. The electronic conduction of the resulting molecular junction is extremely sensitive to the chemical nature of the molecule. Therefore designing this latter correctly allows the implementation of a given function inside the molecular junction. Throughout the chapter different approaches are reviewed, from hybrid devices to quantum molecular logic gates. We particularly stress that one can implement an entire logic circuit in a single molecule, using either classical-like intramolecular connections, or a deformation of the molecular orbitals induced by a conformational change of the molecule. These approaches are radically different from the hybrid-device approach, where several molecules are connected together to build the circuit.

Manipulating molecular quantum states with classical metal atom inputs: demonstration of a single molecule NOR logic gate

Quantum states of a trinaphthylene molecule were manipulated by putting its naphthyl branches in contact with single Au atoms. One Au atom carries 1-bit of classical information input that is converted into quantum information throughout the molecule. The Au-trinaphthylene electronic interactions give rise to measurable energy shifts of the molecular electronic states demonstrating a NOR logic gate functionality. The NOR truth table of the single molecule logic gate was characterized by means of scanning tunnelling spectroscopy.

Supramolecular architectures on surfaces formed through hydrogen bonding optimized in three dimensions

Supramolecular self-assembly on surfaces, guided by hydrogen bonding interactions, has been widely studied, most often involving planar compounds confined directly onto surfaces in a planar two-dimensional (2-D) geometry and equipped with structurally rigid chemical functionalities to direct the self-assembly. In contrast, so-called molecular Landers are a class of compounds that exhibit a pronounced three-dimensional (3-D) structure once adsorbed on surfaces, arising from a molecular backboard equipped with bulky groups which act as spacer legs. Here we demonstrate the first examples of extended, hydrogen-bonded surface architectures formed from molecular Landers. Using high-resolution scanning tunnelling microscopy (STM) under well controlled ultrahigh vacuum conditions we characterize both one-dimensional (1-D) chains as well as five distinct long-range ordered 2-D supramolecular networks formed on a Au(111) surface from a specially designed Lander molecule equipped with dual diamino-triazine (DAT) functional moieties, enabling complementary NH...N hydrogen bonding. Most interestingly, comparison of experimental results to STM image calculations and molecular mechanics structural modeling demonstrates that the observed molecular Lander-DAT structures can be rationalized through characteristic intermolecular hydrogen bonding coupling motifs which would not have been possible in purely planar 2-D surface assembly because they involve pronounced 3-D optimization of the bonding configurations. The described 1-D and 2-D patterns of Lander-DAT molecules may potentially be used as extended molecular molds for the nucleation and growth of complex metallic nanostructures.

Large molecules on surfaces: deposition and intramolecular STM manipulation by directional forces

Intramolecular manipulation of single molecules on a surface with a scanning tunnelling microscope enables the controlled modification of their structure and, consequently, their physical and chemical properties. This review presents examples of intramolecular manipulation experiments with rather large molecules, driven by directional, i.e. chemical or electrostatic, forces between tip and molecule. It is shown how various regimes of forces can be explored and characterized with one and the same manipulation of a single molecule by changing the tip-surface distance. Furthermore, different deposition techniques under ultrahigh vacuum conditions are discussed because the increasing functionality of such molecules can lead to fragmentation during the heating step, making their clean deposition difficult.

Step-by-step rotation of a molecule-gear mounted on an atomic-scale axis

Gears are microfabricated down to diameters of a few micrometres. Natural macromolecular motors, of tens of nanometres in diameter, also show gear effects. At a smaller scale, the random rotation of a single-molecule rotor encaged in a molecular stator has been observed, demonstrating that a single molecule can be rotated with the tip of a scanning tunnelling microscope (STM). A self-assembled rack-and-pinion molecular machine where the STM tip apex is the rotation axis of the pinion was also tested. Here, we present the mechanics of an intentionally constructed molecule-gear on a Au(111) surface, mounting and centring one hexa-t-butyl-pyrimidopentaphenylbenzene molecule on one atom axis. The combination of molecular design, molecular manipulation and surface atomic structure selection leads to the construction of a fundamental component of a planar single-molecule mechanical machine. The rotation of our molecule-gear is step-by-step and totally under control, demonstrating nine stable stations in both directions.

Conformational Adaptation and Selective Adatom Capturing of Tetrapyridyl-porphyrin Molecules on a Copper (111) Surface

We present a combined low-temperature scanning tunneling microscopy and near-edge X-ray adsorption fine structure study on the interaction of tetrapyridyl-porphyrin (TPyP) molecules with a Cu(111) surface. A novel approach using data from complementary experimental techniques and charge density calculations allows us to determine the adsorption geometry of TPyP on Cu(111). The molecules are centered on "bridge" sites of the substrate lattice and exhibit a strong deformation involving a saddle-shaped macrocycle distortion as well as considerable rotation and tilting of the meso-substituents. We propose a bonding mechanism based on the pyridyl-surface interaction, which mediates the molecular deformation upon adsorption. Accordingly, a functionalization by pyridyl groups opens up pathways to control the anchoring of large organic molecules on metal surfaces and tune their conformational state. Furthermore, we demonstrate that the affinity of the terminal groups for metal centers permits the selective capture of individual iron atoms at low temperature.

A rack-and-pinion device at the molecular scale

Molecular machines, and in particular molecular motors with synthetic molecular structures and fuelled by external light, voltage or chemical conversions, have recently been reported. Most of these experiments are carried out in solution with a large ensemble of molecules and without access to one molecule at a time, a key point for future use of single molecular machines with an atomic scale precision. Therefore, to experiment on a single molecule-machine, this molecule has to be adsorbed on a surface, imaged and manipulated with the tip of a scanning tunnelling microscope (STM). A few experiments of this type have described molecular mechanisms in which a rotational movement of a single molecule is involved. However, until now, only uncontrolled rotations or indirect signatures of a rotation have been reported. In this work, we present a molecular rack-and-pinion device for which an STM tip drives a single pinion molecule at low temperature. The pinion is a 1.8-nm-diameter molecule functioning as a six-toothed wheel interlocked at the edge of a self-assembled molecular island acting as a rack. We monitor the rotation of the pinion molecule tooth by tooth along the rack by a chemical tag attached to one of its cogs.

Scanning tunneling spectroscopy simulations of poly(3-dodecylthiophene) chains adsorbed on highly oriented pyrolytic graphite

We report on a hybrid scheme to perform efficient and accurate simulations of scanning tunneling spectroscopy (STS) of molecules weakly bonded to surfaces. Calculations are based on a tight binding (TB) technique, including a self-consistent calculation of the electronic structure of the molecule, to predict STS conductance spectra. The use of a local basis makes our model easily applicable to systems with several hundreds of atoms. We performed first-principles density-functional calculations to extract the geometrical and electronic properties of the system. In this way, we can include, in the TB scheme, the effects of structural relaxation upon adsorption on the electronic structure of the molecule. This approach is applied to the study of regioregular poly(3-dodecylthiophene) polymer chains adsorbed on highly oriented pyrolytic graphite. Results of spectroscopic calculations are discussed and compared with recently obtained experimental data.

Chiral Close-Packing of Achiral Star-Shaped Molecules on Solid Surfaces

From the interplay of scanning tunneling microscopy and theoretical calculations, we study the chiral self-assembly of achiral HtB-HBC molecules upon adsorption on the Cu(110) surface. We find that chirality is expressed at two different levels: a +/-5 degrees rotation of the molecular axis with respect to the close-packed direction of the Cu(110) substrate and a chiral close-packed arrangement expected for star-shaped molecules in 2D. Out of the four possible chiral expressions, only two are found to exist due the effect of van der Waals (vdW) interactions forcing the molecules to simultaneously adjust to the atomic template of the substrate geometry and self-assemble in a close-packed geometry.

Deformation of a "rigid" molecule in self-assembled nanostructures

A simple spirobifluorene molecule with pseudotetrahedral structure was investigated for its supposed conformational resilience upon adsorption. Through deposition at room temperature of this molecule on a Cu(111) surface and subsequent observation at 5 K with an ultrahigh vacuum scanning tunneling microscope, this "rigidity" upon physisorption is confirmed. However, an unexpected chemisorbed state was also found with the molecules arranged in trimers. The unique coexistence of physisorbed and chemisorbed states on the same substrate is thus demonstrated at the early stage of self-assembly.

Trapping and moving metal atoms with a six-leg molecule

Putting to work a molecule able to collect and carry adatoms in a controlled way on a surface is a solution for fabricating atomic structures atom by atom. Investigations have shown that the interaction of an organic molecule with the surface of a metal can induce surface reconstruction down to the atomic scale. In this way, well-defined nanostructures such as chains of adatoms, atomic trenches and metal-ligand compounds have been formed. Moreover, the progress in manipulation techniques induced by a scanning tunnelling microscope (STM) has opened up the possibility of studying artificially built molecular-metal atomic scale structures, and allowed the atom-by-atom doping of a single C(60) molecule by picking up K atoms. The present work goes a step further and combines STM manipulation techniques with the ability of a molecule to assemble an atomic nanostructure. We present a well-designed six-leg single hexa-t-butyl-hexaphenylbenzene (HB-HPB) molecule, which collects and carries up to six copper adatoms on a Cu(111) surface when manipulated with a STM tip. The 'HB-HPB-Cu atoms' complex can be further manipulated, bringing its Cu freight to a predetermined position on the surface where the metal atoms can finally be released.