Studying the stepwise assembly of a four component hybrid structure on Au(111)/mica, the pores of a hydrogen bonded bimolecular network of 3,4,9,10-perylenetetracarboxylic diimide (PTCDI) and 1,3,5-triazine-2,4,6-triamine (melamine) were partitioned by three and four-armed molecules based on oligo([biphenyl]-4-ylethynyl)benzene, followed by the templated adsorption of either C60 fullerene or adamantane thiol molecules. The characterisation by ambient scanning tunneling microscopy (STM) reveals that the pore modifiers exhibit dynamics which pronouncedly depend on the molecular structure. The three-armed molecule 1,3,5-tris([1,1′-biphenyl]-4-ylethynyl)benzene (3BPEB) switches between two symmetry equivalent configurations on a time scale fast compared to the temporal resolution of the STM. Derivatisation of 3BPEB by hydroxyl groups substantially reduces the switching rate. For the four-armed molecule configurational changes are observed only occasionally. The observation of isolated fullerenes and small clusters of adamantane thiol molecules, which are arranged in a characteristic fashion, reveals the templating effect of the trimolecular supramolecular network. However, the fraction of compartments filled by guest molecules is significantly below one for both the thermodynamically controlled adsorption of C60 and the kinetically controlled adsorption of the thiol with the latter causing partial removal of the pore modifier. The experiments, on the one hand, demonstrate the feasibility of templating by nested assembly but, on the other hand, also pinpoint the requirement for the energy landscape to be tolerant to variations in the assembly process.

The structure of a chloride terminated copper monolayer electrodeposited onto Au(111) from a CuSO4/KCl electrolyte was investigated ex situ by three complementary experimental techniques (scanning tunneling microscopy (STM), photoelectron spectroscopy (PES), X-ray standing wave (XSW) excitation) and density functional theory (DFT) calculations. STM at atomic resolution reveals a stable, highly ordered layer which exhibits a Moiré structure and is described by a (5 × 5) unit cell. The XSW/PES data yield a well-defined position of the Cu layer and the value of 2.16 Å above the topmost Au layer suggests that the atoms are adsorbed in threefold hollow sites. The chloride exhibits some distribution around a distance of 3.77 Å in agreement with the observed Moiré pattern due to a higher order commensurate lattice. This structure, a high order commensurate Cl overlayer on top of a commensurate (1 × 1) Cu layer with Cu at threefold hollow sites, is corroborated by the DFT calculations.

A series of para-oligophenylene mono- and dicarboxylic acids (R-(C6H4)nCOOH, n = 1–3, R = H,COOH) was studied. Adsorbed on Au(111)/mica modified by an underpotential deposited bilayer of Ag, the self-assembled monolayers (SAMs) were analyzed by near-edge X-ray absorption fine structure spectroscopy, X-ray photoelectron spectroscopy, and scanning tunneling microscopy. In all cases SAMs are formed with molecules adopting an upright orientation and anchored to the substrate by a carboxylate. Except benzoic acid, all SAMs could be imaged at molecular resolution, which revealed highly crystalline layers with a dense molecular packing. The structures of the SAMs are described by a rectangular (5 × √3) unit cell for the prevailing phase of the monocarboxylic acids and an oblique () unit cell for the dicarboxylic acids, thus evidencing a pronounced influence of the second COOH moiety on the SAM structure. Density functional theory calculations suggest that hydrogen bonding between the SAM-terminating COOH moieties accounts for the difference. Contrasting other classes of SAMs, the systems studied here are determined by intermolecular interactions whereas molecule–substrate interactions play a secondary role. Thus, eliminating problems arising from the mismatch between the molecular and the substrate lattices, coordinatively bonded carboxylic acids on silver should provide considerable flexibility in the design of SAM structures.

Self-assembled monolayers of biphenyl-3,4′,5-tricarboxylic acid (BPTCA) on Au(111)/mica substrates modified by underpotential deposited layers of Cu and Ag were studied by scanning tunneling microscopy under ambient conditions as well as by synchrotron-based X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy. BPTCA forms distinctly different layers on Ag and Cu due to a pronounced influence of the substrate on the balance of intermolecular and molecule–substrate interactions. On Cu a highly crystalline commensurate row structure is formed, described by a 6 × √3 unit cell, a molecular tilt of 45–50° relative to the surface normal, and a bipodal bidentate adsorption geometry. In contrast, incommensurate row structures are formed on Ag which are characterized by significant waves and kinks, a monopodal bidentate adsorption geometry, and a tilt angle of 25–30°. While BPTCA parallels its smaller homologue, benzene-1,3,5-tricarboxylic acid, with regard to the substrate-specific monopodal and bipodal adsorption geometries, the preparation conditions for the monolayer on Cu and the film structure on Ag are pronouncedly different. The results are discussed in terms of the steric requirements and molecular symmetry of BPTCA.

Trigonal molecules compartmentalise the pores of a honeycomb network of 3,4:9,10-tetracarboxylic diimide (PTCDI) and 1,3,5-triazine-2,4,6-triamine (melamine). Extending the 1,3,5-tri(phenylene-ethynylene)benzene core by a phenyl group allows for a well-defined accommodation of the molecule into two symmetry equivalent positions in the pore. The corresponding styryl or phenylene–ethynylene derivatives exceed the pore size and, thus, impede pore modification.

Self-assembled monolayers (SAMs) of isophthalic acid (IPA) and trimesic acid (TMA) were prepared from solution using Au(111)/mica substrates modified by underpotential deposition (UPD) of Cu and Ag. Ex situ analysis by scanning tunneling microscopy (STM), synchrotron based X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy reveals pronouncedly different film structures for the (1 × 1) Cu and (1 × 1) Ag UPD-modified Au(111)/mica substrates. On Cu, both IPA and TMA form highly crystalline commensurate layers with a characteristic row structure, a significant tilt of the aromatic ring by ∼50° from the surface normal and a bipodal adsorption geometry of the molecules involving two carboxylate moieties. In contrast, a significantly smaller tilt angle of ∼20° and a monopodal adsorption geometry is found on Ag. Even though a row structure is also observed for TMA on Ag, it lacks the regularity and, thus, commensurability found on Cu. Contrasting the other systems which yield molecularly resolved STM images, no lateral order is seen in the IPA SAMs despite the fact that both the IPA and TMA layers on Ag have analogous structures with essentially the same tilt angle of the benzene ring. The difference between IPA and TMA on Ag is explained by the difference in the number of carboxyl groups available for stabilising the layer via intermolecular hydrogen bonds.

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The structure of self-assembled monolayers (SAMs) of 3-(4′-(methylthio)-[1,1′-biphenyl]-4-yl)propane-1-thiol (CH3S(C6H4)2(CH2)3SH) formed on Au(111)/mica has been investigated by scanning tunneling microscopy (STM), high-resolution X-ray photoemission spectroscopy (HRXPS), near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and density functional theory (DFT) calculations. A highly crystalline monolayer terminated by thioether moieties is formed, which adopts a structure that differs from the previously studied CH3 terminated analogue with its 2√3 × √3 unit cell. An oblique 2√3 × √61 chiral unit cell containing 8 molecules is proposed. Accommodation of the substantial mismatch between the lattices of the SAM and substrate is explained by molecular design. Serving as a buffer layer, the alkane spacer decouples the SAM lattice, defined by the functionalized aromatic moieties, from the substrate.

1,7-Diadamantanethioperylene-3,4:9,10-tetracarboxylic diimide, (Ad-S)2–PTCDI, adsorbed on Au(111) from solution was investigated by scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS). (Ad-S)2–PTCDI forms a well-ordered monolayer whose structure is described by a (2√63 × √19)R19.1° chiral unit cell containing four molecules. Codeposition of (Ad-S)2–PTCDI with 1,3,5-triazine-2,4,6-triamine (melamine) yields a honeycomb network whose (7√3 × 7√3)R30° unit cell is identical to the unsubstituted PTCDI/melamine analogue. The effect of the adamantyl thioether moieties on the adsorption of guest molecules is investigated using adamantane thiol and C60. While the thioether units do not affect the packing of adamantane thiol molecules a pronounced influence is seen in the case of fullerene. Pore modification involving different combinations of enantiomers of (Ad-S)2–PTCDI give rise to distinctly different arrangements of C60 molecules. The diversity of patterns is further increased by the presence of unsubstituted PTCDI molecules.

Self-assembled monolayers (SAMs) of isophthalic acid (IPA) and trimesic acid (TMA) formed on Cu modified Au(111) substrates by adsorption from aqueous solution were characterised by synchrotron-based X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure spectroscopy (NEXAFS) and scanning tunneling microscopy (STM). Applying the layer-by-layer (LbL) method, the initial stages of growth of metal–organic coordination layers from Cu-acetate and TMA has been studied by STM. Both IPA and TMA SAMs exhibit a row structure with the aromatic units tilted by about 45° with respect to the surface normal. The average distance between rows is 3 × Au–Au distance (= 8.67 Å) with, however, slight variations between different rows. For IPA a very regular pattern is observed giving rise to a rectangular (9 × √3) unit cell containing three molecules. Combining all data a structure is suggested where the molecules are tilted and azimuthally rotated. The variation in the inter-row distance is explained by correlated tilts and rotations in opposite directions. STM studies of the first two LbL deposition cycles reveal predominantly disordered nucleation at domain boundaries. The observation of epitaxial features is explained to arise from a particular combination of molecular orientation in adjacent rows.

The electrodeposition of Pd onto self-assembled monolayers (SAMs) of 3-(4-pyridine-4-ylphenyl)propane-1-thiol on Au(111) has been investigated by scanning tunneling microscopy. Two schemes are compared: One involves an established two-step procedure where Pd2+ ions are first coordinated to the pyridine moieties and subsequently reduced in Pd2+-free electrolyte. The second deposition routine involves electroreduction in an electrolyte containing low concentration of Pd2+ which merges both steps and, thus, significantly simplifies metal deposition onto pyridine-terminated SAMs. Both strategies produce identical Pd nanoparticles (NPs) which exhibit a narrow size distribution and an apparent STM height of ∼2.4 nm. The observation of a Coulomb blockade and easy displacement of the nanoparticles in STM experiments evidence deposition on top of the SAM. The NPs are concluded to be essentially spherical. Growth of the NPs is found to be self-limiting since repeating the complexation−deposition cycle increases the density of the nanoparticles rather than their size but only close to full coverage. At high concentration of the Pd2+ electrolyte, deposition on top of the SAM is impeded by a competitive mushroom-type growth.

Anisotropy of intermolecular and molecule–substrate interactions holds the key to controlling the arrangement of fullerenes into 2D self-assembled monolayers (SAMs). The chemical reactivity of fullerenes allows functionalization of the carbon cages with sulfur-containing groups, thiols and thioethers, which facilitates the reliable adsorption of these molecules on gold substrates. A series of structurally related molecules, eight of which are new fullerene compounds, allows systematic investigation of the structural and functional parameters defining the geometry of fullerene SAMs. Scanning tunnelling microscopy (STM) measurements reveal that the chemical nature of the anchoring group appears to be crucial for the long-range order in fullerenes: the assembly of thiol-functionalized fullerenes is governed by strong molecule–surface interactions, which prohibit formation of ordered molecular arrays, while thioether-functionalized fullerenes, which have a weaker interaction with the surface than the thiols, form a variety of ordered 2D molecular arrays owing to noncovalent intermolecular interactions. A linear row of fullerene molecules is a recurring structural feature of the ordered SAMs, but the relative alignment and the spacing between the fullerene rows is strongly dependent on the size and shape of the spacer group linking the fullerene cage and the anchoring group. Careful control of the chemical functionality on the carbon cages enables positioning of fullerenes into at least four different packing arrangements, none of which have been observed before. Our new strategy for the controlled arrangement of fullerenes on surfaces at the molecular level will advance the development of practical applications for these nanomaterials.

Assembly of dodecyl thiocyanate (C12SCN) from ethanol solution onto Au(111)/mica substrates was investigated by scanning tunneling microscopy (STM), near edge X-ray absorption fine structure spectroscopy (NEXAFS), X-ray photoelectron spectroscopy (XPS), and infrared reflection−absorption spectroscopy (IRRAS). Contrary to previous reports, thiolate monolayers formed by cleavage of the S−CN bond can be obtained whose quality is at least as good as that of self-assembled monolayers (SAMs) formed directly from the thiol analogue of C12SCN, dodecanethiol (C12SH). However, the achievable quality is strikingly dependent on the purity of the thiocyanate with even low levels of contamination impeding the formation of structurally well-defined monolayers.

Self-assembled monolayers (SAMs) of a bis(pyrazol-1-yl)pyridine-substituted thiol (bpp-SH) on Au (111)/mica were studied with scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and near-edge X-ray absorption fine structure spectroscopy (NEXAFS). Using substrates precoated with perylene-3,4,9,10-tetracarboxylic acid dianhydride (PTCDA), preparation at elevated temperatures yields highly ordered layers whose structure is described by a rectangular (5 × √3) unit cell containing one molecule. The bis(pyrazol-1-yl)pyridine (bpp) units exhibit π-stacking along the ⟨112̅⟩ direction, and they are tilted significantly. We conclude the three imine nitrogen atoms in the bpp headgroup adopt a trans,trans arrangement.

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Self-assembled monolayers (SAMs) of isophthalic acid (IPA) and trimesic acid (TMA) formed on Cu modified Au(111) substrates by adsorption from aqueous solution were characterised by synchrotron-based X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure spectroscopy (NEXAFS) and scanning tunneling microscopy (STM). Applying the layer-by-layer (LbL) method, the initial stages of growth of metal–organic coordination layers from Cu-acetate and TMA has been studied by STM. Both IPA and TMA SAMs exhibit a row structure with the aromatic units tilted by about 45° with respect to the surface normal. The average distance between rows is 3 × Au–Au distance (= 8.67 Å) with, however, slight variations between different rows. For IPA a very regular pattern is observed giving rise to a rectangular (9 × √3) unit cell containing three molecules. Combining all data a structure is suggested where the molecules are tilted and azimuthally rotated. The variation in the inter-row distance is explained by correlated tilts and rotations in opposite directions. STM studies of the first two LbL deposition cycles reveal predominantly disordered nucleation at domain boundaries. The observation of epitaxial features is explained to arise from a particular combination of molecular orientation in adjacent rows.

Self-assembled monolayers (SAMs) of isophthalic acid (IPA) and trimesic acid (TMA) were prepared from solution using Au(111)/mica substrates modified by underpotential deposition (UPD) of Cu and Ag. Ex situ analysis by scanning tunneling microscopy (STM), synchrotron based X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy reveals pronouncedly different film structures for the (1 × 1) Cu and (1 × 1) Ag UPD-modified Au(111)/mica substrates. On Cu, both IPA and TMA form highly crystalline commensurate layers with a characteristic row structure, a significant tilt of the aromatic ring by ∼50° from the surface normal and a bipodal adsorption geometry of the molecules involving two carboxylate moieties. In contrast, a significantly smaller tilt angle of ∼20° and a monopodal adsorption geometry is found on Ag. Even though a row structure is also observed for TMA on Ag, it lacks the regularity and, thus, commensurability found on Cu. Contrasting the other systems which yield molecularly resolved STM images, no lateral order is seen in the IPA SAMs despite the fact that both the IPA and TMA layers on Ag have analogous structures with essentially the same tilt angle of the benzene ring. The difference between IPA and TMA on Ag is explained by the difference in the number of carboxyl groups available for stabilising the layer via intermolecular hydrogen bonds.

Trigonal molecules compartmentalise the pores of a honeycomb network of 3,4:9,10-tetracarboxylic diimide (PTCDI) and 1,3,5-triazine-2,4,6-triamine (melamine). Extending the 1,3,5-tri(phenylene-ethynylene)benzene core by a phenyl group allows for a well-defined accommodation of the molecule into two symmetry equivalent positions in the pore. The corresponding styryl or phenylene–ethynylene derivatives exceed the pore size and, thus, impede pore modification.

1,7-Diadamantanethioperylene-3,4:9,10-tetracarboxylic diimide, (Ad-S)2–PTCDI, adsorbed on Au(111) from solution was investigated by scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS). (Ad-S)2–PTCDI forms a well-ordered monolayer whose structure is described by a (2√63 × √19)R19.1° chiral unit cell containing four molecules. Codeposition of (Ad-S)2–PTCDI with 1,3,5-triazine-2,4,6-triamine (melamine) yields a honeycomb network whose (7√3 × 7√3)R30° unit cell is identical to the unsubstituted PTCDI/melamine analogue. The effect of the adamantyl thioether moieties on the adsorption of guest molecules is investigated using adamantane thiol and C60. While the thioether units do not affect the packing of adamantane thiol molecules a pronounced influence is seen in the case of fullerene. Pore modification involving different combinations of enantiomers of (Ad-S)2–PTCDI give rise to distinctly different arrangements of C60 molecules. The diversity of patterns is further increased by the presence of unsubstituted PTCDI molecules.