Molecule-substrate Interactions Research Articles

Comparing Adsorption of an Electron-Rich Triphenylene Derivative: Metallic vs Graphitic Surfaces.

Crucial to the performance of devices based on organic molecules is an understanding of how the substrate-molecule interface influences both structural and electronic properties of the molecular layers. Within this context we studied the self-assembly of an alkoxy-triphenylene derived electron donor (HAT) in the monolayer regime on graphene/Ni(111). The molecules assembled into a close-packed hexagonal network commensurate with the graphene layer. Despite the commensurate structure, the HAT molecules only had a weak, physisorptive interaction with the substrate as pointed out by the photoelectron spectroscopy data. We discuss these findings in view of our recent reports for HAT adsorbed on Ag(111) and graphene/Ir(111). For all three substrates HAT adopts a similar close-packed hexagonal structure commensurate with the substrate while being physisorbed. The ionization potential is equal for all three substrates, supporting weak molecule-substrate interactions. These findings are remarkable, as commensurate overlayers usually only form at strongly interacting interfaces. We discuss potential reasons for this particular behavior of HAT which clearly sets itself apart from most studied molecule-substrate systems. In particular, these are the relatively weak but flexible intermolecular interactions, the molecular symmetry matching that of the substrate, and the comparatively weak but directional molecule-substrate interactions.

Inhibition performance of a novel quinoxaline derivative for carbon steel corrosion in 1 M HCl

In this work, the effect of a new quinoxaline derivative, 2-phenyl-3-(prop-2-yn-1-yloxy) quinoxaline (PYQX), was evaluated as a corrosion inhibitor for carbon steel (CS) in 1 M HCl electrolyte. Weight loss measurement, atomic absorption spectroscopy, potentio­dynamic polarization, electrochemical impedance spectroscopy, scanning electron microscopy with energy dispersive spectroscopy, and UV-vis spectroscopy were employed to assess the inhibitory activity. The electronic properties of the interaction between the inhibitor molecule and the CS substrate were studied using molecular dynamics (MD) simulation, density functional theory (DFT), and Fukui functions. According to AC impedance experiments, the inhibitor under consideration showed a maximum level of 98.1 % inhibition efficiency at 1 mM and 30 °C. The Langmuir adsorption isotherm model explains the adsorption of PYQX on the CS surface. A slope of 1 denotes a strong molecule-substrate interaction, suggesting that the binding occurs at specific surface locations. To understand the functioning of the adsorption mechanism, various thermodynamic and activation parameters were evaluated. PDP tests demonstrated that PYQX functions as a mixed-type inhibitor. Computational correlations (DFT, MD, and Fukui indices) supported the experimental findings.

Sputter-cleaning modified interfacial energetic and molecular structure of DNTT thin film on ITO substrate

The effect of natural electrode contamination on interfacial energetic, structure and morphology of π-conjugated organic molecular layers were studied by depositing dinapthothienothiophene (DNTT) thin films of varying thickness on indium-tin-oxide (ITO) substrates and by using photoelectron spectroscopy, atomic force microscopy and X-ray reflectivity techniques. The DNTT thin film on unclean-ITO surface shows a smaller threshold ionization potential (by ∼0.4 eV) compared to the film on clean-ITO one. A molecule–substrate interaction, present in the DNTT/clean-ITO system, gives rise to an interfacial dipole and charge transfer, presumably through flat-lying seed-layer at the interface. On further deposition, the interfacial coverage increases, while the molecules on top of the seed-layer take different orientation (mostly edge-on) to form highly-dewetted fibrous-islands of very high-thickness but very low-coverage. Overall, the growth of DNTT film on clean-ITO surface is layer-plus-island-like or Stranski–Krastanov-type. On the other hand, the contamination layer at the DNTT/unclean-ITO interface is found to act as a spacer layer, which reduces the intimate molecule–substrate interaction and also the roughness to give rise an edge-on ordered island-like or Volmer–Weber-type film-growth with reduced hole injection barrier (by ∼0.2 eV) and better (almost double) film-coverage to make it a more efficient hole injector compared to the clean interface one.

Manipulating Molecular Self-Assembly Process at the Solid-Liquid Interface Probed by Scanning Tunneling Microscopy.

The phenomenon of ordered self-assembly on solid substrates is a topic of interest in both fundamental surface science research and its applications in nanotechnology. The regulation and control of two-dimensional (2D) self-assembled supra-molecular structures on surfaces have been realized through applying external stimuli. By utilizing scanning tunneling microscopy (STM), researchers can investigate the detailed phase transition process of self-assembled monolayers (SAMs), providing insight into the interplay between intermolecular weak interactions and substrate-molecule interactions, which govern the formation of molecular self-assembly. This review will discuss the structural transition of self-assembly probed by STM in response to external stimuli and provide state-of-the-art methods such as tip-induced confinement for the alignment of SAM domains and selective chirality. Finally, we discuss the challenges and opportunities in the field of self-assembly and STM.

Zinc dialkyldithiophosphates adsorption and dissociation on ferrous substrates: An ab initio study

Zinc dialkyldithiophosphates (ZDDPs) have been commonly used as anti-wear additives in the automotive industry for the past 80 years. Despite their widespread use, a general agreement on their primary functioning mechanism is still lacking. The morphology and composition of the ZDDPs phosphate-based tribofilm, which is essential for its lubricant functioning, have been widely studied experimentally. However, the formation process and the relevant driving forces are still largely debated. In particular, it is unclear whether the stress-induced molecular dissociation occurs in the bulk oil or on the substrate. In this work, we employ ab initio density-functional theory simulations to compare ZDDP fragmentation in vacuum and over a reactive substrate, considering the effects of surface oxidation on the dissociation path. To do so, we developed a computational protocol to study the effects of shear stress on molecules. Our results show that the molecular dissociation is endothermic in the absence of a supporting substrate, while in the presence of an iron substrate, it becomes highly energetically favoured. Moreover, the presence of the substrate changes the reaction path, inducing the detachment of organophosphorus units from Zn-S ones. At the same time, surface oxidation reduces the molecule–substrate interaction. These findings provide valuable insights into the early stages of the formation of phosphate-based tribofilms.

In-Plane Hydrogen Bonds and Out-of-Plane Dipolar Interactions in Self-Assembled Melem Networks

Melem (2,6,10-triamino-s-heptazine) is the building block of melon, a carbon nitride (CN) polymer that is proven to produce H2 from water under visible illumination. With the aim of bringing additional insight into the electronic structure of CN materials, we performed a spectroscopic characterization of gas-phase melem and of a melem-based self-assembled 2D H-bonded layer on Au(111) by means of ultraviolet and X-ray photoemission spectroscopy (UPS, XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. In parallel, we performed density functional theory (DFT) simulations of the same systems to unravel the molecular charge density redistribution caused by the in-plane H-bonds. Comparing the experimental results with the spectroscopic DFT simulations, we can correlate the induced charge accumulation on the Namino atoms to the red-shift of the corresponding N 1s binding energy (BE) and of the Namino 1s → LUMO+n transitions. Moreover, when introducing a supporting Au(111) surface in the computational simulations, we observe a molecule–substrate interaction that almost exclusively involves the out-of-plane molecular orbitals, leaving those engaged in the in-plane H-bonded network rather unperturbed.

Self‐Guided Growth of Electronically Decoupled C60 on Graphene on Rh(110)

AbstractThe authors report on the behavior of C60 molecules adsorbed on graphene (Gr) monolayers grown on Rh(110), studied by means of scanning tunneling microscopy and spectroscopy under ultra‐high vacuum conditions. Fullerene molecules form a well‐ordered close packed hexagonal layout with an intermolecular distance of ≈1 nm. As demonstrated from the experimental data, the molecular packing direction of C60 is locally close to being aligned with the quasi‐1D moiré patterns formed by graphene on the metal support. Moreover, for certain orientations of graphene on Rh(110), the underlying moiré pattern appears superimposed on the molecular assembly. However, the analysis of the highest occupied molecular orbital and the lowest unoccupied molecular orbital structures and the differential conductance curves of C60 on Gr/Rh(110) suggest a weak molecule–substrate interaction, similar to other 2D material/metal interfaces. All these observations can imply that the moiré structures of Gr/Rh(110) play a central role in the arrangement of C60, but without modifying its electronic properties, which makes this Gr/Rh(110) system a singular platform for C60 adsorption. Complementarily, the structural properties of multilayer growth of C60 on Gr/Rh(110) are also investigated.

Influence of local chemical environment and external perturbations of porphyrins on surfaces

Porphyrins and tetrapyrroles play crucial roles in biological processes such as photosynthesis and molecular transport. These nature-based molecules have found application in artificial systems, such as sensing, catalysis, and 2D/3D networks. They are ideal building blocks due to their chemical diversity, stability, and ability to self-assemble on surfaces. Derivatization of the peripheral positions allows for the rational design of magnetic, catalytic, and photochemical properties. Due to this, porphyrins have been used in a variety of natural and artificial systems such as photodynamic therapies and dye-sensitized solar cells. Recently, much work and attention have focused on using specific porphyrin and molecular relatives for molecular electronics due to their robust nature, functionality, and synthesis. The focus of this review is to summarize the mechanisms that affect the internal structure and properties of the molecules and how changes in the local chemical environment alter the electronic properties of the porphyrin. We review the current state of the literature concerning the intermolecular and surface-adsorbate interactions that dictate self-assembly. We will assess the effects that molecule-molecule and molecule-substrate interactions play on the molecule’s properties and the effects that external forces have on the molecular properties. The goal of this review is to dissect the mechanisms responsible for the unique properties that arise from porphyrinic systems adsorbed on surfaces.

Molecular properties of PTCDA on graphene grown on a rectangular symmetry substrate

The chemical modulation associated with moiré patterns, arising at the interface of metal-supported 2D material systems, affects the interaction between molecules and 2D materials on surfaces. Since the crystallography of the support influences the interfacial chemistry of the moiré modulation, this parameter could also play a role in the graphene-molecule interaction, although studies using non-hexagonal metal supports are needed to investigate this effect. It is a key issue since graphene appears combined with organic films in most technological advances related to this material. Here, we have characterized the properties of PTCDA molecules on graphene grown on Rh(110) substrates, which exhibit a rectangular atomic packing, using scanning tunneling microscopy and spectroscopy. The results showed that PTCDA molecules are arranged on the surface into a herringbone structure exhibiting a long-range ordering, which grows continuously across substrate atomic steps edge and dislocations. The quasi-1D moiré patterns of the Gr/Rh(110) surfaces are found to provide an inert chemical landscape for the molecular arrangement. Bias voltage-dependent imaging of the orbital structure of PTCDA molecules and differential conductance spectra back up a weak molecule–substrate interaction scheme. Finally, the α-polymorph of bulk crystal PTCDA has been determined as the favored stacking configuration for bilayer molecules on Gr/Rh(110).

Interaction between pentacene molecules and monolayer transition metal dichalcogenides.

Using first-principles calculations based on density-functional theory, we investigated the adsorption of pentacene molecules on monolayer two-dimensional transition metal dichalcogenides (TMD). We considered the four most popular TMDs, namely, MoS2, MoSe2, WS2 and WSe2, and we examined the structural and electronic properties of pentacene/TMD systems. We discuss how monolayer pentacene interacts with the TMDs, and how this interaction affects the charge transfer and work function of the heterostructure. We also analyse the type of band alignment formed in the heterostructure and how it is affected by molecule-molecule and molecule-substrate interactions. Such analysis is valuable since pentacene/TMD heterostructures are considered to be promising for application in flexible, thin and lightweight photovoltaics and photodetectors.

Influence of core size on self-assembled molecular networks composed of C3h-symmetric building blocks through hydrogen bonding interactions: structural features and chirality.

The effect of the core size on the structure and chirality of self-assembled molecular networks was investigated using two aromatic carboxylic acid derivatives with frameworks displaying C3h symmetry, triphenylene derivative H3TTCA and dehydrobenzo[12]annulene (DBA) derivative DBACOOH, each having three carboxy groups per molecule. Scanning tunneling microscopy observations at the 1-heptanoic acid/graphite interface revealed H3TTCA exclusively forming a chiral honeycomb structure, and DBACOOH forming three structures (type I, II, and III structures) depending on its concentration and whether the system is subjected to annealing treatment. Hydrogen bonding interaction patterns and chirality were carefully analyzed based on a modeling study using molecular mechanics simulations. Moreover, DBACOOH forms chiral honeycomb structures through the co-adsorption of guest molecules. Structural diversity observed for DBACOOH is attributed to its relatively large core size, with this feature modulating the balance between molecule-molecule and molecule-substrate interactions.

A multi-faceted structural, thermodynamic, and spectroscopic approach for investigating ethanol dehydration over transition phase aluminas.

Understanding the role that the surface of a material plays in the mediation of a chemical reaction at the atomic level is paramount to the optimization and improvement of catalytic materials. While this area of research has matured over several decades, few techniques are sensitive enough to directly examine and differentiate the behavior of molecular adsorbates during the course of the chemical reaction with a substrate. In this study, a combined approach which involves structural characterization techniques, volumetric adsorption, temperature programmed desorption, and inelastic neutron scattering (INS) was used to investigate the mechanism of ethanol dehydration on the surface of transition phase aluminas. The alumina samples employed were extensively characterized using X-ray diffraction, solid-state 27Al nuclear magnetic resonance spectroscopy, and thermogravimetric analysis with differential scanning calorimetry. A high-precision volumetric adsorption apparatus was used to characterize the surface area and to controllably dose ethanol onto the surface of the aluminas. A modified temperature programmed desorption (TPD) method which samples the molecular composition of the vapor at discrete temperatures in a closed cell is described. INS results were used to confirm adsorption of ethanol on γ- and θ-alumina and show the reaction of ethanol and subsequent formation of ethylene as a function of temperature. The TPD and INS results affirm that the dehydration reaction and subsequent formation of ethylene on both γ- and θ-aluminas occur rapidly at 300 °C, though ethanol is still observed on θ-alumina indicating fewer active sites. These results demonstrate the value of a multi-faceted characterization approach, featuring INS, towards providing a detailed understanding of the ethanol dehydration mechanism on θ-alumina and further provide the basis for extending this approach to other systems in heterogeneous catalysis and areas where molecule-substrate interactions are poorly understood.

Tuning the odd-even effect on two-dimensional assemblies of curcumin derivatives by alkyl chain substitution: a scanning tunnelling microscopy study.

Well-ordered molecular arrangement on surfaces is fundamental for fabrication of functional molecular devices which are of particular interest in nanotechnology. In addition to nano-manufacturing, the production of useful materials from natural resources has recently attracted increasing attention. Herein, we focused on the two-dimensional (2D) self-assemblies of curcumin derivatives. The effects of the number, length, and substitution of the alkyl chains on the 2D structures of curcumin derivatives were studied by scanning tunnelling microscopy at the highly oriented pyrolytic graphite/1,2,4-trichlorobenzene interface. Curcumin derivatives containing both methoxy and alkoxy chain groups and those possessing four alkoxy chains exhibit linear structures with and without interdigitation of alkoxy chains, respectively. These 2D structure formations are independent of the alkyl chain length. However, the bisdemethoxycurcumin derivatives periodically form stair-like and linear structures depending on the alkyl chain length, which indicates the existence of the odd-even effect. These results suggest that the 2D structural modulation of curcumin derivatives caused by the odd-even effect can be tuned by the number of alkyl chain substituents. The appearance and disappearance of the odd-even effect in curcumin derivatives are discussed in terms of the balance between intermolecular and molecule-substrate interactions.

Exploring the impact of the nitrogen layer on a Cu(001) substrate on the spin crossover properties of [Fe(SalEen-I)2]Br: A DFT study

This work investigates the impact of the Cu:N ratio in the nitrogen layer of a Cu(001) substrate coated with [Fe(SalEen-I)2]Br, an Fe(III) spin crossover (SCO) molecule. Specifically, we probe Cu/Cu(001), Cu3N/Cu(001), Cu2N/Cu(001), and CuN/Cu(001) substrates. To explore the molecule-substrate interaction, density functional theory calculations with Hubbard-U correction (DFT + U) and van der Waals interactions were conducted. From the analysis of the electronic structure, we propose that Cu2N/Cu(001) is the best candidate due to its weak chemical bonding to the adsorbed molecule and preservation of SCO bistability. Based on the total-energy calculations of various adsorption geometries and binding sites, the iodine atoms of the molecule adsorbed diagonally on copper atoms of the Cu2N(001) surface in the low-spin state is the most stable configuration. The energy difference between the high- and low-spin states of this configuration is 8.48 kJ/mol, which is significantly decreased compared to that of the free molecule of 29.14 kJ/mol.

Influence of Molecular Configurations on the Desulfonylation Reactions on Metal Surfaces.

On-surface synthesis is a powerful methodology for the fabrication of low-dimensional functional materials. The precursor molecules usually anchor on different metal surfaces via similar configurations. The activation energies are therefore solely determined by the chemical activity of the respective metal surfaces. Here, we studied the influence of the detailed adsorption configuration on the activation energy on different metal surfaces. We systematically studied the desulfonylation homocoupling for a molecular precursor on Au(111) and Ag(111) and found that the activation energy is lower on inert Au(111) than on Ag(111). Combining scanning tunneling microscopy observations, synchrotron radiation photoemission spectroscopy measurements, and density functional theory calculations, we elucidate that the phenomenon arises from different molecule-substrate interactions. The molecular precursors anchor on Au(111) via Au-S interactions, which lead to weakening of the phenyl-S bonds. On the other hand, the molecular precursors anchor on Ag(111) via Ag-O interactions, resulting in the lifting of the S atoms. As a consequence, the activation barrier of the desulfonylation reactions is higher on Ag(111), although silver is generally more chemically active than gold. Our study not only reports a new type of on-surface chemical reaction but also clarifies the influence of detailed adsorption configurations on specific on-surface chemical reactions.

Two-dimensional dynamic perylene ordering on Ag(110)

We present a room temperature STM study of dynamics of the quasi-liquid perylene monolayer formed on Ag(110) under thermal equilibrium. We observe that the thermodynamic balance of the molecule–molecule and molecule–substrate interactions generates a compact two-dimensional (2D) quasi-liquid state established by mobile perylene molecules dynamically distributed into three distinct motion modes. Monitoring of the quasi-liquid monolayer indicates that each motion mode is triggered by spontaneous recognition of specific locations of the substrate lattice into which transient locking occurs. Analysis of the STM topographies shows that the substrate lattice guides the whole molecule ensemble and provides each of the modes with a distinct register. In each mode, the substrate registry forces the transiently immobile molecules to alternate with the transiently mobile ones. The dynamic interminglement of the modes prevents segregation of the dynamically active and inactive molecules. The substrate provides memory to the intermingled molecules and eliminates ergodicity of the quasi-liquid state. Fourier transform of the topographies unravels the long-range spatial correlations and epitaxial character of the quasi-liquid state. Analysis of the short-range mode coupling allows us to understand the mechanism of the long-range mode coupling. The substrate force field induces the dynamical ergodic–non-ergodic phase transition giving rise to the stationary long-range ordered −12.532 quasi-liquid state.

Improved order and transport in C60 thin films grown on SiO2 via use of transient templates

The performance of C60 semiconducting films is linked to the degree of crystallinity and ordering, properties that strongly depend on the substrate, and growth conditions. Substrate–molecule interactions can be specifically tailored by employing growth templates to achieve a desired thin film structure. However, the presence of a growth template after the film deposition is usually not desirable as it may change the properties of the layer of interest. The ability to remove a growth template without any disruption to the active layer would be highly beneficial. A simple method of template removal by annealing is presented here. A variety of small organic molecules (perfluoropentacene, [6]phenacene, and α-sexithiophene) were used as a growth template to obtain a high-quality well-ordered C60 thin film. In situ grazing-incidence wide-angle x-ray scattering was employed to study the structural changes of C60 thin films during template removal. While a slight disturbance of the thin film structure was observed during template removal caused by evaporated molecules from the growth template escaping through the C60 layer, the disruption is only temporary. When the annealing process is concluded, only the well-ordered C60 thin film directly on top of SiO2 is left, which is not achievable without the use of a growth template. Improved crystallinity and grain size of such a thin film, when compared to preparation without a growth template, lead to a significant improvement of the charge carrier mobility. Importantly, template removal prevents the formation of undesired ambipolar transistor characteristics.

Arsenic Monolayers Formed by Zero-Dimensional Tetrahedral Clusters and One-Dimensional Armchair Nanochains.

One-dimensional (1D) arsenene nanostructures are predicted to host a variety of interesting physical properties including antiferromagnetic, semiconductor-semimetal transition and quantum spin Hall effect, which thus holds great promise for next-generation electronic and spintronic devices. Herein, we devised a surface template strategy in a combination with surface-catalyzed decomposition of molecular As4 cluster toward the synthesis of the superlattice of ultranarrow armchair arsenic nanochains in a large domain on Au(111). In the low annealing temperature window, zero-dimensional As4 nanoclusters are assembled into continuous films through intermolecular van der Waals and molecule-substrate interactions. At the elevated temperature, the subsequent surface-assisted decomposition of molecular As4 nanoclusters leads to the formation of a periodic array of 1D armchair arsenic nanochains that form a (2 × 3) superstructure on the Au(111) surface. These ultranarrow armchair arsenic nanochains are predicted to have a small bandgap of ∼0.50 eV, in contrast to metallic zigzag chains. In addition, the Au-supported arsenic nanochains can be flipped to form a bilayer structure through tip indentation and manipulation, suggesting the possible transfer of these nanochains from the substrate. The successful realization of arsenic nanostructures is expected to advance low-dimensional physics and infrared optoelectronic nanodevices.

Superatom Molecular Orbitals of Li@C60: Effects of the Li Position and the Substrate

Understanding the character of superatom molecular orbitals (SAMOs) of fullerenes, especially those of the endohedral fullerenes, can potentially facilitate the utility of these molecules in organic electronics beyond conventional limits. However, the detailed nature of SAMOs in molecular films on substrates has yet to be unraveled. Using density functional theory, we investigate the wavefunction distributions and electronic structures of SAMO states of a Li@C60 monolayer in dependence on the position of Li within the cage and the type of substrate species. We find that the characteristics of the SAMOs in terms of shape and energy are quite sensitive to the Li position due to different charge redistributions. The substrate affects the intermolecular distances in the Li@C60 films and modifies the widths and dispersion of the SAMO bands while retaining energetics similar to that of the isolated Li@C60 monolayer. The substrate also affects the SAMO effective masses, making it possible to tune them via substrate-induced interaction. A properly chosen substrate can so be beneficial for Li confinement and SAMO stability, reflecting the molecule–substrate interaction and the charge transfer at the interface. These findings provide insights into the design and engineering of SAMOs of molecular films.

Formation and structural characterization of two-dimensional wetting water layer on graphite (0001).

Understanding the structure and wettability of monolayer water is essential for revealing the mechanisms of nucleation, growth, and chemical reactivity at interfaces. We have investigated the wetting layer formation of water (ice) on the graphite (0001) surface using a combination of low-energy electron diffraction (LEED) and scanning tunneling microscopy (STM). At around monolayer coverages, the LEED pattern showed a (2 × 2) periodicity and STM revealed a hydrogen-bonded hexagonal network. The lattice constant was about 9% larger than that for ice Ih/Ic crystals, and the packing density was 0.096 Å-2. These results indicate that an extended ice network is formed on graphite, different from that on metal surfaces. Graphite is hydrophobic under ambient conditions due to the airborne contaminant but is considered inherently hydrophilic for a clean surface. In this study, the hydrophilic nature of the clean surface has been investigated from a molecular viewpoint. The formation of a well-ordered commensurate monolayer supports that the interaction of water with graphite is not negligible so that a commensurate wetting layer is formed at the weak substrate-molecule interaction limit.