Adsorption of Large Hydrocarbons on Coinage Metals: A van der Waals Density Functional Study

Possibilities and Limitations of Kinetic Studies in On-Surface Synthesis by Real Time X-ray Photoelectron Spectroscopy

The kinetics of coupling reactions on surfaces can be quantitatively studied in real time by X-ray Photoelectron Spectroscopy (XPS). From fitting experimental data, kinetic reaction parameters such as the rate constant's pre-exponential and activation energy can be deduced and compared to quantum chemical simulations. To elucidate the possibilities and limitations of this approach, we propose studies in which experimental data are first simulated and subsequently fitted. Knowing the exact kinetic parameters used in the simulation allows one to evaluate the accuracy of the fit result. Here, several experimental influences, such as the data point density and the addition of noise, are explored for a model reaction with first-order kinetics. The proposed procedure sheds light on the accuracy with which kinetic parameters can be derived and may also help in the design of future experiments.

Mechanistic insights into on-surface reactions from isothermal temperature-programmed X-ray photoelectron spectroscopy

On-surface synthesis often proceeds under kinetic control due to the irreversibility of key reaction steps, rendering kinetic studies pivotal. The accurate quantification of reaction rates also bears potential for unveiling reaction mechanisms. Temperature-Programmed X-ray Photoelectron Spectroscopy (TP-XPS) has emerged as an analytical tool for kinetic studies with splendid chemical and sufficient temporal resolution. Here, we demonstrate that the common linear temperature ramps lead to fitting ambiguities. Moreover, pinpointing the reaction order remains intricate, although this key parameter entails information on atomistic mechanisms. Yet, TP-XPS experiments with a stepped temperature profile comprised of isothermal segments facilitate the direct quantification of rate constants from fitting time courses. Thereby, rate constants are obtained for a series of temperatures, which allows independent extraction of both activation energies and pre-exponentials from Arrhenius plots. By using two analogous doubly versus triply brominated aromatic model compounds, we found that their debromination on Ag(111) is best modeled by second-order kinetics and thus proceeds via the involvement of a second, non-obvious reactant. Accordingly, we propose that debromination is activated by surface supplied Ag adatoms. This hypothesis is supported by Density Functional Theory (DFT) calculations. We foresee auspicious prospects for this TP-XPS variant for further exploring the kinetics and mechanisms of on-surface reactions.

Studying the adsorption of emerging organic contaminants in zeolites with dispersion-corrected density functional theory calculations: From numbers to recommendations

Adsorption energies obtained from dispersion-corrected density functional theory (DFT) calculations show a considerable dependence on the choice of exchange-correlation functional and dispersion correction. A number of investigations have employed different approaches to compute adsorption energies of small molecules in zeolites, using reference values from high-level calculations and/or experiments. Such comparative studies are lacking for larger functional organic molecules such as pharmaceuticals or personal care products, despite their potential relevance for applications, e. g., in contaminant removal or drug delivery. The present study aims to fill this gap by comparing adsorption energies and, for selected cases, equilibrium structures of emerging organic contaminants adsorbed in MOR- and FAU-type all-silica zeolites. A total of 13 dispersion-corrected DFT approaches are compared, including methods using a pairwise dispersion correction as well as non-local van der Waals density functionals. While absolute values of adsorption energies vary widely, qualitative trends across the set of zeolite-guest combinations are not strongly dependent on the choice of functional. For selected cluster models, DFT adsorption energies are compared to reference values from coupled cluster (DLPNO-CCSD(T)) calculations. Although all DFT approaches deliver systematically more negative adsorption energies than the coupled cluster reference, this tendency is least pronounced for the rev-vdW-DF2 functional.

On-surface synthesis of enetriynes

Belonging to the enyne family, enetriynes comprise a distinct electron-rich all-carbon bonding scheme. However, the lack of convenient synthesis protocols limits the associated application potential within, e.g., biochemistry and materials science. Herein we introduce a pathway for highly selective enetriyne formation via tetramerization of terminal alkynes on a Ag(100) surface. Taking advantage of a directing hydroxyl group, we steer molecular assembly and reaction processes on square lattices. Induced by O₂ exposure the terminal alkyne moieties deprotonate and organometallic bis-acetylide dimer arrays evolve. Upon subsequent thermal annealing tetrameric enetriyne-bridged compounds are generated in high yield, readily self-assembling into regular networks. We combine high-resolution scanning probe microscopy, X-ray photoelectron spectroscopy and density functional theory calculations to examine the structural features, bonding characteristics and the underlying reaction mechanism. Our study introduces an integrated strategy for the precise fabrication of functional enetriyne species, thus providing access to a distinct class of highly conjugated π-system compounds.

Adsorption of Carbamazepine in All-Silica Zeolites Studied with Density Functional Theory Calculations

The anticonvulsant drug carbamazepine (-) is an emerging contaminant of considerable concern due to its hazard potential and environmental persistence. Previous experimental studies proposed hydrophobic zeolites as promising adsorbents for the removal of carbamazepine from water, but only a few framework types were considered in those investigations. In the present work, electronic structure calculations based on dispersion-corrected density functional theory (DFT) were used to study the adsorption of CBZ in eleven all-silica zeolites having different pore sizes and connectivities of the pore system (AFI, ATS, BEA, CFI, DON, FAU, IFR, ISV, MOR, SFH, SSF framework types). It was found that some zeolites with one-dimensional channels formed by twelve-membered rings (IFR, AFI) exhibit the highest affinity towards CBZ. A "good fit" of CBZ into the zeolite pores that maximizes dispersion interactions was identified as the dominant factor determining the interaction strength. Further calculations addressed the role of temperature (for selected systems) and of guest-guest interactions between coadsorbed CBZ molecules. In addition to predicting zeolite frameworks of particular interest as materials for selective CBZ removal, the calculations presented here also contribute to the atomic-level understanding of the interaction of functional organic molecules with all-silica zeolites.

Dehydrogenation versus deprotonation of disaccharide molecules in vacuum: a thorough theoretical investigation

Dehydrogenation and deprotonation of sucrose and trehalose molecules in vacuum is theoretically studied by using ab initio calculations in the framework of the density functional theory. The differences in the structural, electronic, energetic and vibrational properties of dehydrogenated and deprotonated molecules are discussed, depending on the site from which the hydrogen atom or the proton has been removed. The dehydrogenated molecules are found to be stable, regardless of which hydrogen atom is removed. This contrasts with the instability of the deprotonated molecules, where break-ups or structural reorganizations of the molecule are observed in 20-30% of the cases, but only when the hydrogen atom whose proton is removed was bonded to a carbon atom. Considering the stability and possible rearrangements of the hydrogen network of the deprotonated/dehydrogenated molecule, the formation of additional hydrogen-bridge bonds compared with the nominal molecule appears to be more pronounced for the deprotonated molecules than for the dehydrogenated ones. Moreover, our calculations show that the hydrogen-transfer energy barriers are usually larger for the deprotonated molecules than for the dehydrogenated ones. Finally, compared with the nominal molecule, the vibrational frequency spectrum is shifted to lower frequencies for both the dehydrogenated and the deprotonated molecules.

Surface-Assisted Synthesis of N-Containing π-Conjugated Polymers

On-surface synthesis has recently emerged as a powerful strategy to design conjugated polymers previously precluded in conventional solution chemistry. Here, an N-containing pentacene-based precursor (tetraazapentacene) is ex-professo synthesized endowed with terminal dibromomethylene (:CBr₂ ) groups to steer homocoupling via dehalogenation on metallic supports. Combined scanning probe microscopy investigations complemented by theoretical calculations reveal how the substrate selection drives different reaction mechanisms. On Ag(111) the dissociation of bromine atoms at room temperature triggers the homocoupling of tetraazapentacene units together with the binding of silver adatoms to the nitrogen atoms of the monomers giving rise to a N-containing conjugated coordination polymer (P1). Subsequently, P1 undergoes ladderization at 200 °C, affording a pyrrolopyrrole-bridged conjugated polymer (P2). On Au(111) the formation of the intermediate polymer P1 is not observed and, instead, after annealing at 100 °C, the conjugated ladder polymer P2 is obtained, revealing the crucial role of metal adatoms on Ag(111) as compared to Au(111). Finally, on Ag(100) the loss of :CBr2 groups affords the formation of tetraazapentacene monomers, which coexist with polymer P1. Our results contribute to introduce protocols for the synthesis of N-containing conjugated polymers, illustrating the selective role of the metallic support in the underlying reaction mechanisms.

Evolution of adsorption heights in the on-surface synthesis and decoupling of covalent organic networks on Ag(111) by normal-incidence X-ray standing wave

Structural characterization in on-surface synthesis is primarily carried out by Scanning Probe Microscopy (SPM) which provides high lateral resolution. Yet, important fresh perspectives on surface interactions and molecular conformations are gained from adsorption heights that remain largely inaccessible to SPM, but can be precisely measured with both elemental and chemical sensitivity by Normal-Incidence X-ray Standing Wave (NIXSW) analysis. Here, we study the evolution of adsorption heights in the on-surface synthesis and post-synthetic decoupling of porous covalent triazine-phenylene networks obtained from 2,4,6-tris(4-bromophenyl)-1,3,5-triazine (TBPT) precursors on Ag(111). Room temperature deposition of TBPT and mild annealing to ∼150 °C result in full debromination and formation of organometallic intermediates, where the monomers are linked into reticulated networks by C-Ag-C bonds. Topologically identical covalent networks comprised of triazine vertices that are interconnected by biphenyl units are obtained by a thermally activated chemical transformation of the organometallic intermediates. Exposure to iodine vapor facilitates decoupling by intercalation of an iodine monolayer between the covalent networks and the Ag(111) surface. Accordingly, Scanning Tunneling Microscopy (STM), X-ray Photoelectron Spectroscopy (XPS) and NIXSW experiments are carried out for three successive sample stages: organometallic intermediates, covalent networks directly on Ag(111) and after decoupling. NIXSW analysis facilitates the determination of adsorption heights of chemically distinct carbon species, i.e. in the phenyl and triazine rings, and also for the organometallic carbon atoms. Thereby, molecular conformations are assessed for each sample stage. The interpretation of experimental results is informed by Density Functional Theory (DFT) calculations, providing a consistent picture of adsorption heights and molecular deformations in the networks that result from the interplay between steric hindrance and surface interactions. Quantitative adsorption heights, i.e. vertical distances between adsorbates and surface, provide detailed insight into surface interactions, but are underexplored in on-surface synthesis. In particular, the direct comparison with an in situ prepared decoupled state unveils the surface influence on the network structure, and shows that iodine intercalation is a powerful decoupling strategy.

vdW-DF-ahcx: a range-separated van der Waals density functional hybrid

Hybrid density functionals replace a fraction of an underlying generalized-gradient approximation (GGA) exchange description with a Fock-exchange component. Range-separated hybrids (RSHs) also effectively screen the Fock-exchange component and thus open the door for characterizations of metals and adsorption at metal surfaces. The RSHs are traditionally based on a robust GGA, such as PBE (Perdew J Pet al1996Phys. Rev. Lett.773865), for example, as implemented in the HSE design (Heyd Jet al2003J. Chem. Phys.1188207). Here we define an analytical-hole (Henderson T Met al2008J. Chem. Phys.128194105) consistent-exchange RSH extension to the van der Waals density functional (vdW-DF) method (Berland Ket al2015Rep. Prog. Phys.78066501), launching vdW-DF-ahcx. We characterize the GGA-type exchange in the vdW-DF-cx version (Berland K and Hyldgaard P 2014Phys. Rev. B89035412), isolate the short-ranged exchange component, and define the new vdW-DF hybrid. We find that the performance vdW-DF-ahcx compares favorably to (dispersion-corrected) HSE for descriptions of bulk (broad molecular) properties. We also find that it provides accurate descriptions of noble-metal surface properties, including CO adsorption.

Manipulable Metal Catalyst for Nanographene Synthesis

Performing bottom-up synthesis by using molecules adsorbed on a surface is an effective method to yield functional polycyclic aromatic hydrocarbons (PAHs) and nanocarbon materials. The intramolecular cyclodehydrogenation of hydrocarbons is a critical process in this synthesis; however, thus far, its elementary steps have not been elucidated thoroughly. In this study, we utilize the metal tip of a low-temperature noncontact atomic force microscope as a manipulable metal surface to locally activate dehydrogenation for PAH-forming cyclodehydrogenation. This method leads to the dissociation of a H atom of an intermediate to yield the cyclodehydrogenated product in a target-selective and reproducible manner. We demonstrate the metal-tip-catalyzed dehydrogenation for both benzenoid and nonbenzonoid PAHs, suggesting its universal applicability as a catalyst for nanographene synthesis.

A Comparative Computational Study of the Adsorption of TCNQ and F4-TCNQ on the Coinage Metal Surfaces

The adsorption of tetracyanoquinodimethane and of the closely related derivative tetrafluorotetracyanoquinodimethane on the (111) surfaces of the coinage metals, namely, copper, silver, and (unreconstructed) gold, has been studied by dispersion-corrected ab initio density functional theory calculations. In order to separate the molecule–substrate interaction from the effects of molecule–molecule interaction, only the isolated molecules are considered. The results show that, in this case, the strength of the interaction of both molecules with the surfaces decreases in the expected order Cu > Ag > Au. The total amount of charge transfer, however, behaves in a different way, being larger for Ag and smaller for Cu and Au. This trend can be explained by a combination of the differences in the work functions of the three metals and the amount of backdonation between the molecule and the metal.

Structural analysis of helicene molecules adsorbed on symmetric surfaces

Helicenes are chiral polyaromatic hydrocarbon molecules which self-assemble into ordered monolayers on solid substrates, and are of current interest in the study of supramolecular systems and the development of smart materials. In this work we investigate the geometry of helicene monomers and stacked dimers on (111) facets of coinage metals. The geometry of the adsorbed molecules is shaped by the coupling of intermolecular dispersive forces, intramolecular steric repulsion between end rings and surface-molecule interactions. Thus, binding and stereospecificity outcomes vary broadly depending on the identity of molecule/surface pair. Overall, homochiral interactions are found to be more effective than heterochiral stacking, due to a better fit between the helical structures in like dimers. On a surface, this effect is enhanced by the flattening of surface-proximal molecular rings. However, our results show that the "sandwich" effect of the second molecular layer increases molecular footprints in the first layer, with potentially large implications in monolayer organization and surface commensuration.

Ho-Mediated Alkyne Reactions at Low Temperatures on Ag(111)

Low-temperature approaches to catalytic conversions promise efficiency, selectivity, and sustainable processes. Control over certain coupling reactions can be obtained via the pre-positioning of reactive moieties by self-assembly. However, in the striving field of on-surface synthesis atomistic precision and control remains largely elusive, because the employed coupling reactions proceed at temperatures beyond the thermal stability of the supramolecular templates. Here, utilizing scanning tunneling microscopy, we demonstrate terminal alkyne on-surface reactions mediated by Ho atoms at a weakly reactive Ag(111) substrate at low-temperatures. Density functional theory calculations confirm the catalytic activity of the involved adatoms. Pre-deposited Ho induces alkyne dehydrogenation starting at substrate temperatures as low as 100 K. Ho arriving at molecularly pre-covered surfaces held at 130 and 200 K produces covalent enyne-linked dimers and initiates cyclotrimerization, respectively. Statistical product analysis indicates a two-step pathway for the latter, whereby the enyne intermediates influence the distribution of the products. High chemoselectivity results from the absence of cyclotetramerization and diyne-forming homocoupling. Our analysis indicates that mainly the arriving Ho adatoms enable the coupling. These findings support the concept of dynamic heterogeneity by single-atom catalysts and pave the way for alternative means to control on-surface reactions.

Direct Formation of C-C Double-Bonded Structural Motifs by On-Surface Dehalogenative Homocoupling of gem-Dibromomethyl Molecules

Conductive polymers are of great importance in a variety of chemistry-related disciplines and applications. The recently developed bottom-up on-surface synthesis strategy provides us with opportunities for the fabrication of various nanostructures in a flexible and facile manner, which could be investigated by high-resolution microscopic techniques in real space. Herein, we designed and synthesized molecular precursors functionalized with benzal  gem-dibromomethyl groups. A combination of scanning tunneling microscopy, noncontact atomic force microscopy, high-resolution synchrotron radiation photoemission spectroscopy, and density functional theory calculations demonstrated that it is feasible to achieve the direct formation of C-C double-bonded structural motifs via on-surface dehalogenative homocoupling reactions on the Au(111) surface. Correspondingly, we convert the sp³-hybridized state to an sp²-hybridized state of carbon atoms, i. e., from an alkyl group to an alkenyl one. Moreover, by such a bottom-up strategy, we have successfully fabricated poly(phenylenevinylene) chains on the surface, which is anticipated to inspire further studies toward understanding the nature of conductive polymers at the atomic scale.

Interplay of Chemical and Electronic Structure on the Single-Molecule Level in 2D Polymerization

Single layers of covalently linked organic materials in the form of two-dimensional (2D) polymers constitute structures complementary to inorganic 2D materials. The electronic properties of 2D polymers may be manipulated through a deliberate choice of the organic precursors. Here we address the changes in electronic structure-from precursor molecule to oligomer-by scanning tunneling spectroscopy and ultraviolet photoelectron spectroscopy. For this purpose, we introduce the polymerization reaction of 1,3,5-tris(4-carboxyphenyl)benzene via decarboxylation on Cu(111), which is thoroughly characterized by scanning tunneling microscopy, X-ray photoelectron spectroscopy, and density functional theory calculations. We present a comprehensive study of a contamination-free on-surface coupling scheme and study how dehydrogenation, decarboxylation, and polymerization affect the electronic structure on the molecular level.

Reaction mechanisms for on-surface synthesis of covalent nanostructures

In recent years, on-surface synthesis has become an increasingly popular strategy to form covalent nanostructures. The approach has great prospects for facilitating the manufacture of a range of fascinating materials with atomic precision. However, the on-surface reactions are enigmatic to control, currently restricting its bright perspectives and there is a great need to explore how the reactions are governed. The objective of this topical review is to summarize theoretical work that has focused on comprehending on-surface synthesis protocols through studies of reaction mechanisms.

Quasi one-dimensional band dispersion and surface metallization in long-range ordered polymeric wires

On-surface covalent self-assembly of organic molecules is a very promising bottom-up approach for producing atomically controlled nanostructures. Due to their highly tuneable properties, these structures may be used as building blocks in electronic carbon-based molecular devices. Following this idea, here we report on the electronic structure of an ordered array of poly(para-phenylene) nanowires produced by surface-catalysed dehalogenative reaction. By scanning tunnelling spectroscopy we follow the quantization of unoccupied molecular states as a function of oligomer length, with Fermi level crossing observed for long chains. Angle-resolved photoelectron spectroscopy reveals a quasi-1D valence band as well as a direct gap of 1.15 eV, as the conduction band is partially filled through adsorption on the surface. Tight-binding modelling and ab initio density functional theory calculations lead to a full description of the band structure, including the gap size and charge transfer mechanisms, highlighting a strong substrate-molecule interaction that drives the system into a metallic behaviour.

The gold/ampicillin interface at the atomic scale

In the fight against antibiotic resistance, gold nanoparticles (AuNP) with antibiotics grafted on their surfaces have been found to be potent agents. Ampicillin-conjugated AuNPs have been thus reported to overcome highly ampicillin-resistant bacteria. However, the structure at the atomic scale of these hybrid systems remains misunderstood. In this paper, the structure of the interface between an ampicillin molecule AMP and three flat gold facets Au(111), Au(110) and Au(100) has been investigated with numerical simulations (dispersion-corrected DFT). Adsorption energies, bond distances and electron densities indicate that the adsorption of AMP on these facets goes through multiple partially covalent bonding. The stability of the AuNP/AMP nanoconjugates is explained by large adsorption energies and their potential antibacterial activity is discussed on the basis of the constrained spatial orientation of the grafted antibiotic.

van der Waals forces in density functional theory: a review of the vdW-DF method

A density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology is reviewed. The insights that led to the construction of the Rutgers-Chalmers van der Waals density functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasizing more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only for dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible.

Covalent coupling via dehalogenation on Ni(111) supported boron nitride and graphene

Polymerization of 1,3,5-tris(4-bromophenyl)benzene on graphene and hexagonal boron nitride is investigated by scanning tunnelling microscopy and density functional theory.