Molecule length-induced reentrant self-organization of alkanes in monolayers adsorbed on Au(111)

Exploring adsorption behavior of sulfur and nitrogen compounds on transition metal-doped Cu(100) surfaces: insights from DFT and MD simulations

We conducted an extensive investigation using density functional theory (DFT) calculations and ReaxFF molecular dynamics (MD) simulations to elucidate the mechanisms of desulfurization and denitrogenation on Cu(100) surfaces. This study encompassed both pristine surfaces and those modified with Pt or Rh transition metals. Our primary objective was to gain a deep understanding of the adsorption behavior of thiophene (C4H4S) and pyridine (C5H5N) molecules on stepped Cu(100) surfaces, which serve as models for sulfur and nitrogen compounds. We systematically explored the interplay among water, adsorption efficiency, and surface regeneration capabilities. Using DFT, we thoroughly examined various aspects, including interaction energies, charge transfers, changes in electron density, and alterations in work function upon molecule adsorption. Notably, we observed a decrease in the interaction energy of thiophene, whereas that of pyridine increased when adsorbed on Pt/Rh-doped surfaces compared to pristine ones. Thiophene adsorption reduced the work function, potentially enhancing detectability, without causing inhibitory effects on any surface. Stepped Cu(100) surfaces demonstrated a strong affinity for thiophene, exhibiting an energy difference of approximately 86 kJ mol-1. However, this trend reversed on doped surfaces, where pyridine displayed stronger adsorption than thiophene, resulting in energy differences of around 123 kJ mol-1 and 62 kJ mol-1 on Pt-Cu and Rh-Cu surfaces, respectively. Moreover, our investigation highlighted the regeneration capacity of these surfaces, indicating that all surfaces can be considered promising candidates for desulfurization, while only Cu and Pt-Cu surfaces were found to be suitable for denitrogenation. Furthermore, results from MD simulations in combination with potential of mean force (PMF) simulations at 300 K, aligned with DFT calculations, confirmed the adsorption configurations of pyridine and thiophene. This analysis demonstrated the competitive advantage of thiophene over pyridine in adsorption and highlighted the inhibitory effect of water on pyridine adsorption on the Cu(100) surface.

Spectroscopic imaging of surfaces-Sum frequency generation microscopy (SFGM) combined with compressive sensing (CS) technique

Surface chemistry is notoriously difficult to study, in part, due to the decreased number of molecules that contribute to the properties compared to the bulk phase but often has significant effects on the chemical activity of the material. This is especially true in topics such as corrosion, catalysis, wetting, and many others in nature and industry. Sum frequency generation (SFG) spectroscopy was developed for interface studies due to its high molecular selectivity and surface sensitivity, which is quite useful to study the effects of structural inhomogeneity in microscopy. Compressive sensing (CS) combined with SFG spectroscopy minimizes the imaging time while still producing quality images. Selected systems are presented here to demonstrate the capability of CS-SFG microscopy. CS-SFG microscopy successfully distinguished the static monolayer molecular mixtures, the orientations and adsorption of adsorbed molecules by the dip-coating technique, and the localized CO behaviors on polycrystalline Pt electrodes. Further discussion includes dynamic imaging as a future direction in CS-SFG microscopy. As materials and surfaces become more complex, imaging with chemical contrast becomes indispensable to understanding their performance and CS-SFG microscopy seems highly beneficial in this respect.

Compression-Induced Conformation and Orientation Changes in an n-Alkane Monolayer on a Au(111) Surface

The influence of the preparation method and adsorbed amount of n-tetratetracontane (n-C₄₄H₉₀) on its orientation in a monolayer on the Au(111) surface is studied by near carbon K-edge X-ray absorption fine structure spectroscopy (C K-NEXAFS), scanning tunneling microscopy (STM) under ultrahigh vacuum, and infrared reflection-absorption spectroscopy (IRAS) at the electrochemical interface in sulfuric acid solution. The n-C₄₄H₉₀ molecules form self-assembled lamellar structures with the chain axis parallel to the surface, as observed by STM. For small amounts adsorbed, the carbon plane is parallel to the surface (flat-on orientation). An increase in the adsorbed amount by ∼10-20% induces compression of the lamellar structure either along the lamellar axis or alkyl chain axis. The compressed molecular arrangement is observed by STM, and induced conformation and orientation changes are confirmed by in situ IRAS and C K-NEXAFS.

Alkyl-Based Surfactants at a Liquid Mercury Surface: Computer Simulation of Structure, Self-Assembly, and Phase Behavior

Self-assembled organic films on liquid metals feature a very rich phase behavior, which qualitatively differs from the one on crystalline metals. In contrast to conventional crystalline supports, self-assembled alkylthiol monolayers on liquid metals possess a considerably higher degree of molecular order, thus enabling much more robust metal-molecule-semiconductor couplings for organic electronics applications. Yet, compared to crystalline substrates, the self-assembly of organic surfactants on liquid metals has been studied to a much lesser extent. In this Letter we report the first of its kind molecular simulation investigation of alkyl-based surfactants on a liquid mercury surface. The focus of our investigation is the surfactant conformations as a function of surface coverage and surfactant type. First, we consider normal alkanes because these systems set the basis for simulations of all other organic surfactants on liquid mercury. Subsequently, we proceed with the discussion of alkylthiols that are the most frequently used surfactants in the surface science of hybrid organometallic interfaces. Our results indicate a layering transition of normal alkanes as well as alkylthiols from an essentially bare substrate to a completely filled monolayer of laying molecules. As the surface coverage increases further, we observe a partial wetting of the laying monolayer by the bulk phase of alkanes. In the case of alkylthiols, we clearly see the coexistence of molecules in laying-down and standing-up conformations, in which the sulfur headgroups of the thiols are chemically bound to mercury. In the standing-up phase, the headgroups form an oblique lattice. For the first time we were able to explicitly characterize the molecular-scale structure and transitions between phases of alkyl-based surfactants and to demonstrate how the presence of a thiol headgroup qualitatively changes the phase equilibrium and structure in these systems. The observed phenomena are consistent with available direct and indirect experimental evidence.

Fingerprinting Electronic Molecular Complexes in Liquid

Predicting the electronic framework of an organic molecule under practical conditions is essential if the molecules are to be wired in a realistic circuit. This demands a clear description of the molecular energy levels and dynamics as it adapts to the feedback from its evolving chemical environment and the surface topology. Here, we address this issue by monitoring in real-time the structural stability and intrinsic molecular resonance states of fullerene (C60)-based hybrid molecules in the presence of the solvent. Energetic levels of C60 hybrids are resolved by in situ scanning tunnelling spectroscopy with an energy resolution in the order of 0.1 eV at room-temperature. An ultra-thin organic spacer layer serves to limit contact metal-molecule energy overlap. The measured molecular conductance gap spread is statistically benchmarked against first principles electronic structure calculations and used to quantify the diversity in electronic species within a standard population of molecules. These findings provide important progress towards understanding conduction mechanisms at a single-molecular level and in serving as useful guidelines for rational design of robust nanoscale devices based on functional organic molecules.

Selection of conformational states in surface self-assembly for a molecule with eight possible pairs of surface enantiomers

Chiral adsorption of a complex molecule with as many as eight possible pairs of surface enantiomers is investigated by STM and the selection of enantiomers is understood by statistical analysis and DFT modelling.

Self-assembly of trithia-9-crown-3 and octathia-24-crown-8 on Au(111) surfaces

Scanning tunneling microscopy images of trithia-9-crown-3 and octathia-24-crown-8 self-assembled monolayers (SAMs) reveal completely different SAM structures for the two kinds of thiacrown molecules at liquid n-tetradecane/Au(111) interface.

Emergence of chirality in hexagonally packed monolayers of hexapentyloxytriphenylene on Au(111): a joint experimental and theoretical study

We investigate the expression of chirality in a monolayer formed spontaneously by 2,3,6,7,10,11-pentyloxytriphenylene (H5T) on Au(111). We resolve its interface morphology by combining scanning tunneling microscopy (STM) with theoretical calculations of intermolecular and interfacial interaction potentials. We observe two commensurate structures. While both of them belong to a hexagonal space group, analogical to the triangular symmetry of the molecule and the hexagonal symmetry of the substrate surface, they surprisingly reveal a 2D chiral character. The corresponding breaking of symmetry arises for two reasons. First it is due to the establishment of a large molecular density on the substrate, which leads to a rotation of the molecules with respect to the molecular network crystallographic axes to avoid steric repulsion between neighboring alkoxy chains. Second it is due to the molecule-substrate interactions, leading to commensurable large crystallographic cells associated with the large size of the molecule. As a consequence, molecular networks disoriented with respect to the high symmetry directions of the substrate are induced. The high simplicity of the intermolecular and molecule-substrate van der Waals interactions leading to these observations suggests a generic character for this kind of symmetry breaking. We demonstrate that, for similar molecular densities, only two kinds of molecular networks are stabilized by the molecule-substrate interactions. The most stable network favors the interfacial interactions between terminal alkoxy tails and Au(111). The metastable one favors a specific orientation of the triphenylene core with its symmetry axes collinear to the Au⟨110⟩. This specific orientation of the triphenylene cores with respect to Au(111) appears associated with an energy advantage larger by at least 0.26 eV with respect to the disoriented core.

Nanoelectrical analysis of single molecules and atomic-scale materials at the solid/liquid interface

Evaluating the built-in functionality of nanomaterials under practical conditions is central for their proposed integration as active components in next-generation electronics. Low-dimensional materials from single atoms to molecules have been consistently resolved and manipulated under ultrahigh vacuum at low temperatures. At room temperature, atomic-scale imaging has also been performed by probing materials at the solid/liquid interface. We exploit this electrical interface to develop a robust electronic decoupling platform that provides precise information on molecular energy levels recorded using in situ scanning tunnelling microscopy/spectroscopy with high spatial and energy resolution in a high-density liquid environment. Our experimental findings, supported by ab initio electronic structure calculations and atomic-scale molecular dynamics simulations, reveal direct mapping of single-molecule structure and resonance states at the solid/liquid interface. We further extend this approach to resolve the electronic structure of graphene monolayers at atomic length scales under standard room-temperature operating conditions.

Oxygen attachment on alkanethiolate SAMs induced by low-energy electron irradiation

Reactions of (18)O2 with self-assembled monolayer (SAM) films of 1-dodecanethiol, 1-octadecanethiol, 1-butanethiol, and benzyl mercaptan chemisorbed on gold were studied by the electron stimulated desorption (ESD) of anionic fragments over the incident electron energy range 2-20 eV. Dosing the SAMs with (18)O2 at 50 K results in the ESD of (18)O(-) and (18)OH(-). Electron irradiation of samples prior to (18)O2 deposition demonstrates that intensity of subsequent (18)O(-) and (18)OH(-) desorption signals increase with electron fluence and that in the absence of electron preirradiation, no (18)O(-) and (18)OH(-) ESD signals are observed, since oxygen is unable to bind to the SAMs. A minimum incident electron energy of 6-7 eV is required to initiate the binding of (18)O2 to the SAMs. O2 binding is proposed to proceed by the formation of CHx-1(•) radicals via resonant dissociative electron attachment and nonresonant C-H dissociation processes. The weaker signals of (18)O(-) and (18)OH(-) from short-chain SAMs are related to the latter's resistance to electron-induced damage, due to the charge-image dipole quenching and electron delocalization. Comparison between the present results and those for DNA oligonucleotides self-assembled on Au (Mirsaleh-Kohan, N. et al. J. Chem. Phys. 2012, 136, 235104) indicates that the oxygen binding mechanism is common to both systems.

Moiré pattern induced by the electronic coupling between 1-octanol self-assembled monolayers and graphite surface

Two-dimensional self-assembly of 1-octanol molecules on a graphite surface is investigated using scanning tunneling microscopy (STM) at the solid/liquid interface. STM images reveal that this molecule self-assembles into a compact hydrogen-bonded herringbone nanoarchitecture. Molecules are preferentially arranged in a head-to-head and tail-to-tail fashion. A Moiré pattern appears in the STM images when the 1-octanol layer is covering the graphite surface. The large Moiré stripes are perpendicular to the 1-octanol lamellae. Interpretation of the STM images suggests that the Moiré periodicity is governed by the electronic properties of the graphite surface and the 1-octanol layer periodicity.

Two-dimensional superstructures and softened C-H stretching vibrations of cyclohexane on Rh(111): effects of preadsorbed hydrogen

Adsorption structures and interaction of cyclohexane molecules on the clean and hydrogen-preadsorbed Rh(111) surfaces were investigated using scanning tunneling microscopy, spot-profile-analysis low-energy electron diffraction, temperature-programmed desorption, and infrared reflection absorption spectroscopy (IRAS). Various ordered structures of adsorbed cyclohexane were observed as a function of hydrogen and cyclohexane coverages. When the fractional coverage (θ(H)) of preadsorbed hydrogen was below 0.8, four different commensurate or higher-order commensurate superstructures were found as a function of θ(H); whereas more densely packed incommensurate overlayers became dominant at higher θ(H). IRAS measurements showed sharp softened C-H vibrational peaks at 20 K, which originate from the electronic interaction between adsorbed cyclohexane and the Rh surface. The multiple softened C-H stretching peaks in each phase are due to the variation in the adsorption distance from the substrate. At high hydrogen coverages they became attenuated in intensity and eventually diminished at θ(H) = 1. The gradual disappearance of the soft mode correlates well with the structural phase transition from commensurate structures to incommensurate structures with increasing hydrogen coverage. The superstructure of adsorbed cyclohexane is controlled by the delicate balance between adsorbate-adsorbate and adsorbate-substrate interactions which are affected by preadsorbed hydrogen.

Surface Nano-Structuring by Adsorption and Chemical Reactions

Nano-structuring of the surface caused by adsorption of molecules or atoms and by the reaction of surface atoms with adsorbed species is reviewed from a chemistry viewpoint. Self-assembly of adsorbed species is markedly influenced by weak mutual interactions and the local strain of the surface induced by the adsorption. Nano-structuring taking place on the surface is well explained by the notion of a quasi-molecule provided by the reaction of surface atoms with adsorbed species. Self-assembly of quasi-molecules by weak internal bonding provides quasi-compounds on a specific surface. Various nano-structuring phenomena are discussed: (i) self-assembly of adsorbed molecules and atoms; (ii) self-assembly of quasi-compounds; (iii) formation of nano-composite surfaces; (iv) controlled growth of nano-materials on composite surfaces. Nano-structuring processes are not always controlled by energetic feasibility, that is, the formation of nano-composite surface and the growth of nano-particles on surfaces are often controlled by the kinetics. The idea of the “kinetic controlled molding” might be valuable to design nano-materials on surfaces.

Experimental three-dimensional description of the liquid hexadecane/graphite interface

By using an atomic force microscope based on a quartz tuning fork sensor, a 3-dimensional description of the interface between liquid hexadecane and a highly oriented pyrolytic graphite surface can be achieved at room temperature. The C16H34 monolayer in contact with the substrate surface exhibits a lamellar structure whereas no observation at the liquid/graphite interface by scanning tunnelling microscopy was reported for this alkane. The second layer shows very weak corrugations corresponding to lamella boundaries. Force/distance curves show at least four oscillations separated by 0.4 nm except for the first period with a 0.38 nm distance that corresponds to the layer closer the substrate. Such a description agrees well with molecular dynamics results obtained on alkane/solid interfaces.

Molecular architectonic on metal surfaces

The engineering of highly organized systems from instructed molecular building blocks opens up new vistas for the control of matter and the exploration of nanodevice concepts. Recent investigations demonstrate that well-defined surfaces provide versatile platforms for steering and monitoring the assembly of molecular nanoarchitectures in exquisite detail. This review delineates the principles of noncovalent synthesis on metal substrates under ultrahigh vacuum conditions and briefly assesses the pertaining terminology-self-assembly, self-organization, and self-organized growth. It presents exemplary scanning-tunneling-microscopy observations, providing atomistic insight into the self-assembly of organic clusters, chains, and superlattices, and the metal-directed assembly of low-dimensional coordination architectures. This review also describes hierarchic-assembly protocols leading to intricate multilevel order. Molecular architectonic on metal surfaces represents a versatile rationale to realize structurally complex nanosystems with specific shape, composition, and functional properties, which bear promise for technological applications.

Structures of 17,19-hexatriacontadiyne monolayers on Au(111) studied by infrared reflection absorption spectroscopy and scanning tunneling microscopy

The aggregation and reaction of 17,19-hexatriacontadiyne molecules are studied on a Au(111) surface. The molecular orientation and arrangement are elucidated by infrared reflection absorption spectroscopy (IRAS) and scanning tunneling microscopy (STM). A vapor-deposited monolayer and a multilayered film formed by adsorption from the solution provide IRA spectra with bands due to the antisymmetric and symmetric stretching of methylenes in the gauche conformation. After the adsorbed film is rinsed with the solvent, however, the spectrum loses the gauche bands and is characterized by the enhanced C-H(distal) and C-H(proximal) stretching bands, which means that all-trans molecules are laid flat. Only STM images for the rinsed film display columnar structures on the herringbones of the reconstructed Au(111) surface; the alkyl chain direction is found to be parallel to the Au atom row. The results indicate that an ordered monolayer is formed first at the liquid-solid interface, and then, disordered overlayers with the gauche conformation are grown but removed by a rinse. Upon exposure to UV light, thus obtained monomer columns are converted into oligomers with flexible backbones and an increased gauche population in the alkyl chains, which resemble red phase polydiacetylenes in LB films.

Electric-field-driven surface aggregation of a model zwitterionic surfactant

Electrochemical measurements, atomic force microscopy, and scanning tunneling microscopy have been combined to describe the electric-field-controlled surface aggregation of N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (DDAPS), a model zwitterionic surfactant, at a Au(111) electrode surface. At concentrations below the critical micelle concentration (CMC), the monomer adsorbs and aggregates at the surface. The charge on the metal (sigmaM) controls the orientation of adsorbed molecules and consequently the film structure. At high negative (sigmaM < -5 microC cm-2) charge densities, a spongy, disordered film is formed in which the polar heads are turned toward the solution. At high positive (sigmaM > +5 microC cm-2) charge densities, a planar film with "blisters" is observed with the polar heads of DDAPS turned to the metal. Hemicylindrical aggregates are observed in the intermediate charge density range (-5 < sigmaM < +5 microC cm-2). At bulk concentrations higher than the CMC, micelles adsorb and the structure of these films is controlled by the fusion of the adsorbed micelles. STM and AFM images provided direct visualization of this field-driven surface aggregation of the zwitterionic surfactant.

Molecular Aggregation within Self-Ordered Monolayers

The monolayer growth of pyrimido-pentaphenylbenzene (NPB) on Cu(111) is investigated by means of low-temperature scanning tunneling microscopy (LT-STM). The pyrimidine side group gives rise to a pronounced resonant tunneling state and, furthermore, affects molecular self-ordering. Different molecular aggregates are formed inside the hexagonal closed packed monolayer. A structure model for the monolayer is proposed and the temperature dependence of this self-ordering process is investigated by varying the preparation temperature between 270 and 370 K. The intermolecular bonding of the aggregates is demonstrated by STM manipulation experiments. Moreover, different aggregations of the molecules induce characteristic energy shifts in the resonant tunneling state, as revealed by means of scanning tunneling spectroscopy.

Coulombic amino group-metal bonding: adsorption of adenine on Cu110

The interaction between molecular amino groups and metal surfaces is analyzed from first-principles calculations using the adsorption of adenine on Cu110 as a model case. The amino group nitrogens are found to adsorb on top of the surface copper atoms. However, the bonding clearly cannot be explained in terms of covalent interactions. Instead, we find it to be largely determined by mutual polarization and Coulomb interaction between substrate and adsorbate.

Self-Assembly of Phospholipid Molecules at a Au(111) Electrode Surface

We described the first scanning tunneling microscopy study of spreading unilamellar vesicles of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) at a Au(111) electrode surface. At the initial stage of the film formation, the molecular resolution images revealed that DMPC molecules are adsorbed flat with the acyl chains oriented parallel to the surface. The molecules assemble into double rows by aligning the acyl chains in the nearest neighbor direction of the reconstructed Au(111) surface and assuming a 90 +/- 10 degrees angle with respect to line of the molecular row. After approximately 30 min, this film is transformed into a hemimicellar state with long rows characteristic for the formation of hemicylindrical surface micelles. At hydrophilic surfaces such as glass, spreading of vesicles involves adsorption, rupture, and sliding of a single bilayer on a lubricating film of the solvent. We have provided the first evidence that a different mechanism is involved in spreading the vesicles at gold. The molecules released by rupture of vesicles self-assemble into an ordered film, and the assembly is controlled by the chain-substrate interaction.

Adsorption and Reactions of C6 Hydrocarbons at High Pressures on Pt(111) Single-Crystal Surfaces Studied by Sum Frequency Generation Vibrational Spectroscopy: Mechanisms of Isomerization and Dehydrocyclization of n-Hexane

The adsorption geometries and surface reactions of various C(6) hydrocarbons (n-hexane, 2-methylpentane, 3-methylpentane, and 1-hexene) adsorbed on Pt(111) were investigated using sum frequency generation (SFG) surface vibrational spectroscopy. The adsorptions and reactions were carried out in 1.5 Torr of C(6) hydrocarbons in the absence and presence of excess hydrogen (15 Torr) and in the temperature range 296-453 K. At 296 K and in the presence of excess hydrogen, n-hexane and 3-methylpentane adsorbed molecularly on Pt(111) mostly in "flat-lying" geometries. Upon heating the sample up to 453 K, the molecules underwent dehydrogenation to form new surface species in "standing-up" geometries, such as hexylidyne and metallacyclic species. However, 2-methylpentane and 1-hexene were dehydrogenated to metallacyclobutane and hexylidyne, respectively, at 296 K in the presence of excess hydrogen. The dehydrogenated species remained unreacted on the surface upon heating the sample up to 453 K. The absence of excess hydrogen enhanced dehydrogenation of n-hexane and 3-methylpentane to form pi-allyl c-C(6)H(9) and metallacyclohexane, respectively, at 296 K. Upon heating to 453 K, the pi-allyl c-C(6)H(9) species underwent irreversible dehydrogenation, while hexylidyne and metallacyclic species remained unreacted. On the basis of these results, the mechanisms for catalytic isomerization and dehydrocyclization of n-hexane, which are the important "reforming" reactions to produce high-octane fuels over platinum, were discussed.

Long-range self-assembly of a polyunsaturated linear organosilane at the n-tetradecane/Au(111) interface studied by STM

We report on the formation of self-assembled monolayers of 13-(trimethylsilyl)-1-tridecene-6,12-diyne [C13H17-Si(CH3)3], an organosilane derivative with a linear polyunsaturated chain, on Au(111) substrates. Molecular resolution STM images recorded at the liquid-solid interface between gold and tetradecane reveal a long-range and densely packed hexagonal lattice with a ( radical3 x radical3)R30 degrees -like structure commensurate against gold adlattice.

Anchoring of organic molecules to a metal surface: HtBDC on Cu(110)

The interaction of largish molecules with metal surfaces has been studied by combining the imaging and manipulation capabilities of the scanning tunneling microscope (STM). At the atomic scale, the STM results directly reveal that the adsorption of a largish organic molecule can induce a restructuring of a metal surface underneath. This restructuring anchors the molecules on the substrate and is the driving force for a self-assembly process of the molecules into characteristic molecular double rows.