Impact of long-range attraction on desorption kinetics.

Desorption of molecules from surfaces is widespread both in nature and technology. Despite its omnipresence and conceptual simplicity, fundamental details can be surprisingly complex and are often poorly understood. In many cases, first-order kinetics is assumed, which implies that the adsorbates do not interact with each other and desorption is the rate-limiting process. While this might be a good approximation in some cases, it is far from reality in the case of adsorbates that form ordered structures. Here, we study the desorption of a submonolayer film of 3-nitrophenol from the natural cleavage plane of calcite kept in ultrahigh vacuum. Interestingly, two distinctly different desorption regimes are observed during isothermal desorption monitored by dynamic atomic force microscopy. Initially, at high coverages, the coverage decreases almost linearly in time, indicating a constant desorption rate. Beyond this linear regime, at low coverages, a drastic increase in desorption rate is observed until the surface is completely empty. The transition between these two regimes is associated with a critical island width. We propose an existence of a long-range attractive interaction between the molecules as a possible explanation for the sudden increase in the desorption rate when a critical island width is reached. The herein observed phenomenon of two different desorption regimes is expected to be of general nature when interactions beyond next-neighbour attraction are present.

Tip-activated single-atom catalysis: CO oxidation on Au adatom on oxidized rutile TiO2 surface.

Single-atom catalysis of carbon monoxide oxidation on metal-oxide surfaces is crucial for greenhouse recycling, automotive catalysis, and beyond, but reports of the atomic-scale mechanism are still scarce. Here, using scanning probe microscopy, we show that charging single gold atoms on oxidized rutile titanium dioxide surface, both positively and negatively, considerably promotes adsorption of carbon monoxide. No carbon monoxide adsorption is observed on neutral gold atoms. Two different carbon monoxide adsorption geometries on gold atoms are identified. We demonstrate full control over the redox state of adsorbed gold single atoms, carbon monoxide adsorption geometry, and carbon monoxide adsorption/desorption by the atomic force microscopy tip. On charged gold atoms, we activate Eley-Rideal oxidation reaction between carbon monoxide and a neighboring oxygen adatom by the tip. Our results provide unprecedented insights into carbon monoxide adsorption and suggest that the gold dual activity for carbon monoxide oxidation after electron or hole attachment is also the key ingredient in photocatalysis under realistic conditions.

Extending on-surface synthesis from 2D to 3D by cycloaddition with C60.

As an efficient molecular engineering approach, on-surface synthesis (OSS) defines a special opportunity to investigate intermolecular coupling at the sub-molecular level and has delivered many appealing polymers. So far, all OSS is based on the lateral covalent bonding of molecular precursors within a single molecular layer; extending OSS from two to three dimensions is yet to be realized. Herein, we address this challenge by cycloaddition between C60 and an aromatic compound. The C60 layer is assembled on the well-defined molecular network, allowing appropriate molecular orbital hybridization. Upon thermal activation, covalent coupling perpendicular to the surface via [4 + 2] cycloaddition between C60 and the phenyl ring of the molecule is realized; the resultant adduct shows frozen orientation and distinct sub-molecular feature at room temperature and further enables lateral covalent bonding via [2 + 2] cycloaddition. This work unlocks an unconventional route for bottom-up precise synthesis of three-dimensional covalently-bonded organic architectures/devices on surfaces.

Super-Robust Xanthine-Sodium Complexes on Au(111).

A widely accepted theory is that life originated from the hydrothermal environment in the primordial ocean. Nevertheless, the low desorption temperature from inorganic substrates and the fragileness of hydrogen-bonded nucleobases do not support the required thermal stability in such an environment. Herein, we report the super-robust complexes of xanthine, one of the precursors for the primitive nucleic acids, with Na. We demonstrate that the well-defined xanthine-Na complexes can only form when the temperature is ≥430 K, and the complexes keep adsorbed even at ≈720 K, presenting as the most thermally stable organic polymer ever reported on Au(111). This work not only justifies the necessity of high-temperature, Na-rich environment for the prebiotic biosynthesis but also reveals the robustness of the xanthine-Na complexes upon the harsh environment. Moreover, the complexes can induce significant electron transfer with the metal as inert as Au and hence lift the Au atoms up.

Cyclic Single Atom Vertical Manipulation on a Nonmetallic Surface.

Motivated by the quest for experimental procedures capable of controlled manipulation of single atoms on surfaces, we set up a computational strategy that explores the cyclical vertical manipulation of a broad set of single atoms on the GaAs(110) surface. First-principles simulations of atomic force microscope tip-sample interactions were performed considering families of GaAs and Au-terminated tip apexes with varying crystalline termination. We identified a subset of tips capable of both picking up and depositing an adatom (Ga, As, Al, and Au) any number of times via a modify-restore cycle that "resets" the apex of the scanning probe to its original structure at the end of each cycle. Manipulation becomes successful within a certain window of lateral and vertical tip distances that are observed to be different for extracting and depositing each atom. A practical experimental protocol of special utility for potential cyclical manipulation of single atoms on a nonmetallic surface is proposed.

Subsurface-Carbon-Induced Local Charge of Copper for an On-Surface Displacement Reaction.

Transition-metal carbides have sparked unprecedented enthusiasm as high-performance catalysts in recent years. Still, the catalytic properties of copper carbide remain unexplored. By introducing subsurface carbon to Cu(111), a displacement reaction of a proton in a carboxyl acid group with a single Cu atom is demonstrated at the atomic scale and room temperature. Its occurrence is attributed to the C-doping-induced local charge of surface Cu atoms (up to +0.30 e/atom), which accelerates the rate of on-surface deprotonation via reduction of the corresponding energy barrier, thus enabling the instant displacement of a proton with a Cu atom when the molecules adsorb on the surface. This well-defined and robust Cuδ+ surface based on subsurface-carbon doping offers a novel catalytic platform for on-surface synthesis.

On-Surface Decarboxylation Coupling Facilitated by Lock-to-Unlock Variation of Molecules upon the Reaction.

On-surface synthesis (OSS) involving relatively high energy barriers remains challenging due to a typical dilemma: firm molecular anchor is required to prevent molecular desorption upon the reaction, whereas sufficient lateral mobility is crucial for subsequent coupling and assembly. By locking the molecular precursors on the substrate then unlocking them during the reaction, we present a strategy to address this challenge. High-yield synthesis based on well-defined decarboxylation, intermediate transition, and hexamerization is demonstrated, resulting in an extended and ordered network exclusively composed of the newly synthesized macrocyclic compound. Thanks to the steric hindrance of its maleimide group, we attain a preferential selection of the coupling. This work unlocks a promising path to enrich the reaction types and improve the coupling selectivity hence the structual homogeneity of the final product for OSS.

Chemical shielding of H2O and HF encapsulated inside a C60 cage.

Molecular surgery provides the opportunity to study relatively large molecules encapsulated within a fullerene cage. Here we determine the location of an H2O molecule isolated within an adsorbed buckminsterfullerene cage, and compare this to the intrafullerene position of HF. Using normal incidence X-ray standing wave (NIXSW) analysis, coupled with density functional theory and molecular dynamics simulations, we show that both H2O and HF are located at an off-centre position within the fullerene cage, caused by substantial intra-cage electrostatic fields generated by surface adsorption of the fullerene. The atomistic and electronic structure simulations also reveal significant internal rotational motion consistent with the NIXSW data. Despite this substantial intra-cage interaction, we find that neither HF or H2O contribute to the endofullerene frontier orbitals, confirming the chemical isolation of the encapsulated molecules. We also show that our experimental NIXSW measurements and theoretical data are best described by a mixed adsorption site model.

Long-range ordered and atomic-scale control of graphene hybridization by photocycloaddition.

Chemical reactions that convert sp2 to sp3 hybridization have been demonstrated to be a fascinating yet challenging route to functionalize graphene. So far it has not been possible to precisely control the reaction sites nor their lateral order at the atomic/molecular scale. The application prospects have been limited for reactions that require long soaking, heating, electric pulses or probe-tip press. Here we demonstrate a spatially selective photocycloaddition reaction of a two-dimensional molecular network with defect-free basal plane of single-layer graphene. Directly visualized at the submolecular level, the cycloaddition is triggered by ultraviolet irradiation in ultrahigh vacuum, requiring no aid of the graphene Moiré pattern. The reaction involves both [2+2] and [2+4] cycloadditions, with the reaction sites aligned into a two-dimensional extended and well-ordered array, inducing a bandgap for the reacted graphene layer. This work provides a solid base for designing and engineering graphene-based optoelectronic and microelectronic devices.

Graphene-Like Covalent Organic Framework with a Wide Band Gap Synthesized On Surface via Stepwise Reactions.

Developing graphene-like two-dimensional materials naturally possessing a band gap has sparked enormous interest. Thanks to the inherent wide band gap and high mobility in the 2D plane, covalent organic frameworks containing triazine rings (t-COFs) hold great promise in this regard, whilst the synthesis of single-layer t-COFs remains highly challenging. Herein, we present the fabrication of a well-defined graphene-like t-COF on Au(111). Instead of single/multiple-step single-type reactions commonly applied for on-surface synthesis, distinct stepwise on-surface reactions, including alkynyl cyclotrimerization, C-O bond cleavage, and C-H bond activation, are triggered on demand, leading to product evolution in a controlled step-by-step manner. Aside from the precise control in sophisticated on-surface synthesis, this work proposes a single-atomic-layer organic semiconductor with a wide band gap of 3.41 eV.

An Endergonic Synthesis of Single Sondheimer-Wong Diyne by Local Probe Chemistry.

Recent advances in scanning probe microscopy on surface enable not only direct observation of molecular structures but also local probe reactions, in which unstable short-lived products have been synthesized and analyzed. Now, an endergonic reaction to synthesize a single Sondheimer-Wong diyne from 6,13-dibromopentaleno[1,2-b:4,5-b']dinaphthalene by local probe chemistry on a ultra-thin film of NaCl formed on a Cu(111) surface at 4.3 K is presented. The structures of the precursor, two intermediates, and the final product were directly identified by the differential conductance imaging with a CO functionalized tip. DFT calculations revealed that the multiple-step reaction, being endergonic overall, is facilitated by temporal charging and discharging of the molecule placed in the nanometric junction between the Cu tip and the Cu substrate underneath the ultra-thin NaCl film. This local probe reaction expands possibilities to synthesize nanocarbon materials in a bottom-up manner.

Externally driven molecular ratchets on a periodic potential surface: a rate equations approach.

The long time dynamics of molecular ratchets on a 1D periodic potential energy surface (PES) subjected to an external stimulus is studied using the rate equation method. The PES consisting of repeated waveforms made of two peaks is considered as an example of a spatially symmetric or asymmetric PES. This PES may, for example, correspond to diffusion of a bipedal molecule that moves along an atomic track via an inchworm walk mechanism [Raval et al., Angew. Chem., Int. Ed., 2015, 54, 7101]. Generalisation to a PES consisting of an arbitrary number of peaks of various heights is straightforward. Assuming the validity of the transition state theory (TST) for the calculation of the transition rates between neighbouring potential wells, the probability of occupying each type of potential well on the PES is obtained analytically, and then the net current for the molecules to move preferentially in a particular direction under application of external fields over a long time is derived. Note that different to methods based on solving numerically the corresponding Fokker-Plank equation, our method is entirely analytical in the limit of weak external fields. The results of the analytical calculations are compared with the exact numerical solution of the derived rate equations. The following external stimuli are considered: constant, sinusoidal and shifted sinusoidal fields due to either a spatially uniform thermal gradient or an electrostatic field. The possible applications of the method for extracting energy from the Brownian motion under load and separating molecules of different chiralities on the surface are also discussed.

Controlling the preferential motion of chiral molecular walkers on a surface.

Molecular walkers standing on two or more "feet" on an anisotropic periodic potential of a crystal surface may perform a one-dimensional Brownian motion at the surface-vacuum interface along a particular direction in which their mobility is the largest. In thermal equilibrium the molecules move with equal probabilities both ways along this direction, as expected from the detailed balance principle, well-known in chemical reactivity and in the theory of molecular motors. For molecules that possess an asymmetric potential energy surface (PES), we propose a generic method based on the application of a time-periodic external stimulus that would enable the molecules to move preferentially in a single direction thereby acting as Brownian ratchets. To illustrate this method, we consider a prototypical synthetic chiral molecular walker, 1,3-bis(imidazol-1-ylmethyl)-5(1-phenylethyl)benzene, diffusing on the anisotropic Cu(110) surface along the Cu rows. As unveiled by our kinetic Monte Carlo simulations based on the rates calculated using ab initio density functional theory, this molecule moves to the nearest equivalent lattice site via the so-called inchworm mechanism in which it steps first with the rear foot and then with the front foot. As a result, the molecule diffuses via a two-step mechanism, and due to its inherent asymmetry, the corresponding PES is also spatially asymmetric. Taking advantage of this fact, we show how the external stimulus can be tuned to separate molecules of different chirality, orientation and conformation. The consequences of these findings for molecular machines and the separation of enantiomers are also discussed.

Correction: Controlling the preferential motion of chiral molecular walkers on a surface.

[This corrects the article DOI: 10.1039/C9SC01135H.].

Tip-Induced Control of Charge and Molecular Bonding of Oxygen Atoms on the Rutile TiO2 (110) Surface with Atomic Force Microscopy.

We study a low-temperature on-surface reversible chemical reaction of oxygen atoms to molecules in ultrahigh vacuum on the semiconducting rutile TiO2(110)-(1 × 1) surface. The reaction is activated by charge transfer from two sources, natural surface/subsurface polarons and experimental Kelvin probe force spectroscopy as a tool for electronic charge manipulation with single electron precision. We demonstrate a complete control over the oxygen species not attainable previously, allowing us to deliberately discriminate in favor of charge or bond manipulation, using either direct charge injection/removal through the tip-oxygen adatom junction or indirectly via polarons. Comparing our ab initio calculations with experiment, we speculate that we may have also manipulated the spin on the oxygens, allowing us to deal with the singlet/triplet complexities associated with the oxygen molecule formation. We show that the manipulation outcome is fully governed by three experimental parameters, vertical and lateral tip positions and the bias voltage.

Measurement and Manipulation of the Charge State of an Adsorbed Oxygen Adatom on the Rutile TiO2(110)-1×1 Surface by nc-AFM and KPFM.

For the first time, the charge states of adsorbed oxygen adatoms on the rutile TiO2(110)-1×1 surface are successfully measured and deliberately manipulated by a combination of noncontact atomic force microscopy and Kelvin probe force microscopy at 78 K under ultrahigh vacuum and interpreted by extensive density functional theory modeling. Several kinds of single and double oxygen adatom species are clearly distinguished and assigned to three different charge states: Oad-/2Oad-, Oad2-/2Oad2-, and Oad--Oad2-, i.e., formal charges of either one or two electrons per atom. Because of the strong atomic-scale image contrast, these states are clearly resolved. The observations are supported by measurements of the short-range force and local contact potential difference as a function of the tip-sample distance as well as simulations. Comparison with the simulations suggests subatomic resolution by allowing us to resolve the rotated oxygen p orbitals. In addition, we manage to reversibly switch the charge states of the oxygen adatoms between the Oad- and Oad2- states, both individually and next to another oxygen, by modulating the frequency shift at constant positive voltage during both charging and discharging processes, i.e., by the tip-induced electric field of one orientation. This work provides a novel route for the investigation of the charge state of the adsorbates and opens up novel prospects for studying transition-metal-oxide-based catalytic reactions.

Phase-field method for epitaxial kinetics on surfaces.

We present a procedure for simulating epitaxial growth based on the phase-field method. We consider a basic model in which growth is initiated by a flux of atoms onto a heated surface. The deposited atoms diffuse in the presence of this flux and eventually collide to form islands which grow and decay by the attachment and detachment of migrating atoms at their edges. Our implementation of the phase-field method for this model includes uniform deposition, isotropic surface diffusion, and stochastic nucleation (in both space and time), which creates islands whose boundaries evolve as the surface atoms "condense" into and "evaporate" from the islands. Computations using this model in the submonolayer regime, prior to any appreciable coalescence of islands, agree with the results of kinetic Monte Carlo (KMC) simulations for the coverage-dependence of adatom and island densities and island-size distributions, for both reversible and irreversible growth. The scaling of the island density, as obtained from homogeneous rate equations, agrees with KMC simulations for irreversible growth and for reversible growth for varying deposition flux at constant temperature. For reversible growth with varying temperature but constant flux, agreement relies on an estimate of the formation energy of the critical cluster. Taken together, our results provide a comprehensive analysis of the phase-field method in the submonolayer regime of epitaxial growth, including the verification of the main scaling laws for adatoms and island densities and the scaling functions for island-size distributions, and point to the areas where the method can be extended and improved.

Formation of Hypoxanthine Tetrad by Reaction with Sodium Chloride: From Planar to Stereo.

By reacting with NaCl on Au(111), the formation of hypoxanthine (HX) tetrads is demonstrated at the atomic scale in real space. These results directly demonstrate that alternative purine tetrads can be formed in both planar and non-planar configuration, and that ionic bonding plays a crucial role for the formation and planar-to-stereo transformation of the tetrads, providing deeper insight for constructing artificial DNA/RNA quadruplexes. Moreover, both the tilted HXs and Na show strong charge transfer with the substrate in the non-planar phase. The insights gained by this work also open up new routes to tune the electrostatic nature of metal-organic interfaces and design stereo-nanostructures on surfaces.

Graphene growth by molecular beam epitaxy: an interplay between desorption, diffusion and intercalation of elemental C species on islands.

The growth of graphene by molecular beam epitaxy from an elemental carbon precursor is a very promising technique to overcome some of the main limitations of the chemical vapour deposition approach, such as the possibility to synthesize graphene directly on a wide variety of surfaces including semiconductors and insulators. However, while the individual steps of the chemical vapour deposition growth process have been extensively studied for several surfaces, such knowledge is still missing for the case of molecular beam epitaxy, even though it is a key ingredient to optimise its performance and effectiveness. In this work, we have performed a combined experimental and theoretical study comparing the growth rate of the molecular beam epitaxy and chemical vapour deposition processes on the prototypical Ir (111) surface. In particular, by employing high-resolution fast X-ray photoelectron spectroscopy, we were able to follow the growth of both single- and multi-layer graphene in real time, and to identify the spectroscopic fingerprints of the different C layers. Our experiments, supported by density functional theory calculations, highlight the role of the interaction between different C precursor species and the growing graphene flakes on the growth rate of graphene. These results provide an overview of the main differences between chemical vapour deposition and molecular beam epitaxy growth and thus on the main parameters which can be tuned to optimise growth conditions.

On-surface synthesis on a bulk insulator surface.

On-surface synthesis has rapidly emerged as a most promising approach to prepare functional molecular structures directly on a support surface. Compared to solution synthesis, performing chemical reactions on a surface offers several exciting new options: due to the absence of a solvent, reactions can be envisioned that are otherwise not feasible due to the insolubility of the reaction product. Perhaps even more important, the confinement to a two-dimensional surface might enable reaction pathways that are not accessible otherwise. Consequently, on-surface synthesis has attracted great attention in the last decade, with an impressive number of classical reactions transferred to a surface as well as new reactions demonstrated that have no classical analogue. So far, the majority of the work has been carried out on conducting surfaces. However, when aiming for electronic decoupling of the resulting structures, e.g. for the use in future molecular electronic devices, non-conducting surfaces are highly desired. Here, we review the current status of on-surface reactions demonstrated on the (10.4) surface of the bulk insulator calcite. Besides thermally induced C-C coupling of halogen-substituted aryls, photochemically induced [2 + 2] cycloaddition has been proven possible on this surface. Moreover, experimental evidence exists for coupling of terminal alkynes as well as diacetylene polymerization. While imaging of the resulting structures with dynamic atomic force microscopy provides a direct means of reaction verification, the detailed reaction pathway often remains unclear. Especially in cases where the presence of metal atoms is known to catalyze the corresponding solution chemistry reaction (e.g. in the case of the Ullmann reaction), disclosing the precise reaction pathway is of importance to understand and generalize on-surface reactivity on a bulk insulator surface. To this end, density-functional theory calculations have proven to provide atomic-scale insights that have greatly contributed to unravelling the details of on-surface synthesis on a bulk insulator surface.