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Describing chain-like assembly of ethoxygroup-functionalized organic molecules on Au(111) using high-throughput simulations.

ABSTRACT: Due to the low corrugation of the Au(111) surface, 1,4-bis(phenylethynyl)-2,5-bis(ethoxy)benzene (PEEB) molecules can form quasi interlocked lateral patterns, which are observed in scanning tunneling microscopy experiments at low temperatures. We demonstrate a multi-dimensional clustering approach to quantify the anisotropic pair-wise interaction of molecules and explain these patterns. We perform high-throughput calculations to evaluate an energy function, which incorporates the adsorption energy of single PEEB molecules on the metal surface and the intermolecular interaction energy of a pair of PEEB molecules. The analysis of the energy function reveals, that, depending on coverage density, specific types of pattern are preferred which can potentially be exploited to form one-dimensional molecular wires on Au(111).

SUBMITTER: Lokamani

PROVIDER: S-EPMC8290052 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Nonintuitive Surface Self-Assembly of Functionalized Molecules on Ag(111).

Project description:The fabrication of nanomaterials involves self-ordering processes of functional molecules on inorganic surfaces. To obtain specific molecular arrangements, a common strategy is to equip molecules with functional groups. However, focusing on the functional groups alone does not provide a comprehensive picture. Especially at interfaces, processes that govern self-ordering are complex and involve various physical and chemical effects, often leading to unexpected structures, as we showcase here on the example of a homologous series of quinones on Ag(111). Naively, one could expect that such quinones, which all bear the same functionalization, form similar motifs. In salient contrast, our joint theoretical and experimental study shows that profoundly different structures are formed. Using a machine-learning-based structure search algorithm, we find that this is due to a shift of the balance of three antagonizing driving forces: adsorbate-substrate interactions governing adsorption sites, adsorbate-adsorbate interactions favoring close packing, and steric hindrance inhibiting certain otherwise energetically beneficial molecular arrangements. The theoretical structures show excellent agreement with our experimental characterizations of the organic/inorganic interfaces, both for the unit cell sizes and the orientations of the molecules within. The nonintuitive interplay of similarly important interaction mechanisms will continue to be a challenging aspect for the design of functional interfaces. With a detailed examination of all driving forces, we are, however, still able to devise a design principle for self-assembly of functionalized molecules.

| S-EPMC8155339 | biostudies-literature

Thioetherification of Br-Mercaptobiphenyl Molecules on Au(111).

Project description:Thioether polymers are fundamental for a variety of applications. Their synthesis is, however, more challenging than that of other metal-catalyzed reactions due to the reported detachment of the S atom during thermal activation. In this study, it has been demonstrated unambiguously that thermal annealing results in the thioetherification of the 4-bromo-4-mercaptobiphenyl molecule (Br-MBP) adsorbed on the surface of Au(111). Through complementary techniques, such as scanning tunneling microscopy, spectroscopy, and first-principle calculations, we have identified four reaction steps, involving sulfhydryl or bromine molecular functional groups and leading to the formation of intermolecular C-S bonds. To form the thioether polymer and to overcome the competitive formation of C-C bonds, two reaction steps, the dehalogenation, and dissociation of the S-Au bond, must occur simultaneously. We detail the electronic properties of the phenyl-sulfur bond and the polymer as a function of the ligand length. This result suggests a wider perspective of this chemical synthesis.

| S-EPMC9951239 | biostudies-literature

Two-Dimensional Self-Assembly Driven by Intermolecular Hydrogen Bonding in Benzodi-7-azaindole Molecules on Au(111).

Project description:The control of molecular structures at the nanoscale plays a critical role in the development of materials and applications. The adsorption of a polyheteroaromatic molecule with hydrogen bond donor and acceptor sites integrated in the conjugated structure itself, namely, benzodi-7-azaindole (BDAI), has been studied on Au(111). Intermolecular hydrogen bonding determines the formation of highly organized linear structures where surface chirality, resulting from the 2D confinement of the centrosymmetric molecules, is observed. Moreover, the structural features of the BDAI molecule lead to the formation of two differentiated arrangements with extended brick-wall and herringbone packing. A comprehensive experimental study that combines scanning tunneling microscopy, high-resolution X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, and density functional theory theoretical calculations has been performed to fully characterize the 2D hydrogen-bonded domains and the on-surface thermal stability of the physisorbed material.

| S-EPMC10291637 | biostudies-literature

Self-assembly of N-heterocyclic carbenes on Au(111).

Project description:Although the self-assembly of organic ligands on gold has been dominated by sulfur-based ligands for decades, a new ligand class, N-heterocyclic carbenes (NHCs), has appeared as an interesting alternative. However, fundamental questions surrounding self-assembly of this new ligand remain unanswered. Herein, we describe the effect of NHC structure, surface coverage, and substrate temperature on mobility, thermal stability, NHC surface geometry, and self-assembly. Analysis of NHC adsorption and self-assembly by scanning tunneling microscopy and density functional theory have revealed the importance of NHC-surface interactions and attractive NHC-NHC interactions on NHC monolayer structures. A remarkable way these interactions manifest is the need for a threshold NHC surface coverage to produce upright, adatom-mediated adsorption motifs with low surface diffusion. NHC wingtip structure is also critical, with primary substituents leading to the formation of flat-lying NHC2Au complexes, which have high mobility when isolated, but self-assemble into stable ordered lattices at higher surface concentrations. These and other studies of NHC surface chemistry will be crucial for the success of these next-generation monolayers.

| S-EPMC8241988 | biostudies-literature

Aurophilic Molecules on Surfaces. Part II. (NapNC)AuCl on Au(111).

Project description:Although aurophilicity is a well-known phenomenon in structural gold chemistry and is found in many crystals of Au(I) complexes, its potential for self-assembly in thin films is not yet explored. This paper is Part II of a study, in which we investigated the ultrathin film formation of chlorido(2-naphthyl isonitrile) gold(I) on gold surfaces. Here, we present the data for the growth of (NapNC)AuCl on isotropic Au(111) surfaces. Already during physical vapor deposition, the condensation of ultrathin films is monitored by photoelectron emission microscopy (PEEM) and incremental and spectrally resolved changes in the optical reflectance (DDRS). Additional structural data obtained by scanning tunneling microscopy (STM) and low-energy electron diffraction (LEED) reveal that the "crossed swords" packing motif known from the bulk is also present in thin films.

| S-EPMC10586446 | biostudies-literature

Chirality variation from self-assembly on Ullmann coupling for the DBCh adsorbate on Au(111) and Ag(111).

Project description:On-surface Ullmann coupling has been considered an appealing approach for the precise fabrication of carbon-based covalent nanostructures under solution-free conditions. However, chirality has seldom been discussed in Ullmann reactions. In this report, self-assembled two-dimensional chiral networks are initially constructed in a large area on Au(111) and Ag(111) after adsorption of the prochiral precursor, 6,12-dibromochrysene (DBCh). Self-assembled phases are then transformed into organometallic (OM) oligomers after debromination, preserving the chirality; in particular, the formation of scarcely reported OM species on Au(111) is discovered herein. With the aryl-aryl bonding induced after intensive annealing, covalent chains are fabricated via the cyclodehydrogenation between chrysene blocks, resulting in the formation of 8-armchair graphene nanoribbons with staggered valleys on both sides. Before chiral polymer chains are constructed by chrysene blocks, the high structural flexibility of OM intermediates on Ag(111) is also revealed during reactions, which is derived from the twofold coordination of Ag atoms and conformationally flexible metal-carbon bonding. Our report not only provides solid evidence of atomically precise fabrication of covalent nanostructures with a feasible bottom-up approach but also sheds insights into the comprehensive investigation of chirality variation from monomers to artificial architectures via surface coupling reactions.

| S-EPMC9972870 | biostudies-literature

Pentacene/perfluoropentacene bilayers on Au(111) and Cu(111): impact of organic-metal coupling strength on molecular structure formation.

Project description:As crucial element in organic opto-electronic devices, heterostructures are of pivotal importance. In this context, a comprehensive study of the properties on a simplified model system of a donor-acceptor (D-A) bilayer structure is presented, using ultraviolet photoelectron spectroscopy (UPS), X-ray photoelectron spectroscopy (XPS), low-energy electron diffraction (LEED) and normal-incidence X-ray standing wave (NIXSW) measurements. Pentacene (PEN) as donor and perfluoropentacene (PFP) as acceptor material are chosen to produce bilayer structures on Au(111) and Cu(111) by sequential monolayer deposition of the two materials. By comparing the adsorption behavior of PEN/PFP bilayers on such weakly and strongly interacting substrates, it is found that: (i) the adsorption distance of the first layer (PEN or PFP) indicates physisorption on Au(111), (ii) the characteristics of the bilayer structure on Au(111) are (almost) independent of the deposition sequence, and hence, (iii) in both cases a mixed bilayer is formed on the Au substrate. This is in striking contrast to PFP/PEN bilayers on Cu(111), where strong chemisorption pins PEN molecules to the metal surface and no intermixing is induced by subsequent PFP deposition. The results illustrate the strong tendency of PEN and PFP molecules to mix, which has important implications for the fabrication of PEN/PFP heterojunctions.

| S-EPMC9419101 | biostudies-literature

Synthesis, electronic properties and self-assembly on Au{111} of thiolated (oligo)phenothiazines.

Project description:(Oligo)phenothiazinyl thioacetates, synthesized by a one-pot sequence, are electrochemically oxidizable and highly fluorescent. SAMs can be readily formed from thiols prepared by in situ deprotection of the thioacetates in the presence of a gold-coated silicon wafer. Monolayer formation is confirmed by ellipsometry and the results compared to those obtained by force field and DFT calculations.

| S-EPMC2919263 | biostudies-literature

Coverage-Dependent Structural Transformation of Cyano-Functionalized Porphyrin Networks on Au(111) via Addition of Cobalt Atoms.

Project description:The self-assembly process of a cobalt-porphyrin derivative (Co-TCNPP) containing cyanophenyl substituents at all four meso positions on Au(111) was studied by means of scanning tunneling microscopy (STM) and low energy electron diffraction (LEED) under ultrahigh vacuum conditions. Deposition of Co-TCNPP onto Au(111) gave rise to the formation of a close-packed H-bonded network, which was independent of coverage as revealed by STM and LEED. However, a coverage-dependent structural transformation took place upon the deposition of Co atoms. At monolayer coverage, a reticulated long-range ordered network exhibiting a distinct fourfold Co coordination was observed. By reduction of the molecular coverage, a second metal-organic coordination network (MOCN) was formed in coexistence with the fourfold Co-coordinated network, that is, a chevron structure stabilized by a simultaneous expression of H-bonding and threefold Co coordination. We attribute the coverage-dependent structural transformation to the in-plane compression pressure exerted by the molecules deposited on the surface. Our study shows that a subtle interplay between the chemical nature of the building blocks (molecules and metallic atoms) and molecular coverage can steer the formation of structurally different porphyrin-based MOCNs.

| S-EPMC6701168 | biostudies-literature

An Electron-Rich Cyclic (Alkyl)(Amino)Carbene on Au(111), Ag(111), and Cu(111) Surfaces.

Project description:The structural properties and binding motif of a strongly σ-electron-donating N-heterocyclic carbene have been investigated on different transition-metal surfaces. The examined cyclic (alkyl)(amino)carbene (CAAC) was found to be mobile on surfaces, and molecular islands with short-range order could be found at high coverage. A combination of scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations highlights how CAACs bind to the surface, which is of tremendous importance to gain an understanding of heterogeneous catalysts bearing CAACs as ligands.

| S-EPMC7496406 | biostudies-literature

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