Steering Self-Assembly of Three-Dimensional Iptycenes on Au(111) by Tuning Molecule-Surface Interactions.

Self-assembly of three-dimensional molecules is scarcely studied on surfaces. Their modes of adsorption can exhibit far greater variability compared to (nearly) planar molecules that adsorb mostly flat on surfaces. This additional degree of freedom can have decisive consequences for the expression of intermolecular binding motifs, hence the formation of supramolecular structures. The determining molecule-surface interactions can be widely tuned, thereby providing a new powerful lever for crystal engineering in two dimensions. Here, we study the self-assembly of triptycene derivatives with anthracene blades on Au(111) by Scanning Tunneling Microscopy, Near Edge X-ray Absorption Fine Structure and Density Functional Theory. The impact of molecule-surface interactions was experimentally tested by comparing pristine with iodine-passivated Au(111) surfaces. Thereby, we observed a fundamental change of the adsorption mode that triggered self-assembly of an entirely different structure.

The Role of Kinetics versus Thermodynamics in Surface-Assisted Ullmann Coupling on Gold and Silver Surfaces.

Surface-assisted Ullmann coupling is the workhorse of on-surface synthesis. Despite its obvious relevance, many fundamental and mechanistic aspects remain elusive. To shed light on individual reaction steps and their progression with temperature, temperature-programmed X-ray photoelectron spectroscopy (TP-XPS) experiments are performed for a prototypical model system. The activation of the coupling by initial dehalogenation is tracked by monitoring Br 3d core levels, whereas the C 1s signature is used to follow the emergence of metastable organometallic intermediates and their conversion to the final covalent products upon heating in real time. The employed 1,3,5-tris(4-bromophenyl)benzene precursor is comparatively studied on Ag(111) versus Au(111), whereby intermolecular bonds and network topologies are additionally characterized by scanning tunneling microscopy (STM). Besides the well-comprehended differences in activation temperatures for debromination, the thermal progression shows marked differences between the two surfaces. Debromination proceeds rapidly on Ag(111), but is relatively gradual on Au(111). While on Ag(111) debromination is well explained by first-order reaction kinetics, thermodynamics prevail on Au(111), underpinned by a close agreement between experimentally deduced and density functional theory (DFT) calculated reaction enthalpies. Thermodynamically controlled debromination on Au(111) over a large temperature range implies an unexpectedly long lifetime of surface-stabilized radicals prior to covalent coupling, as corroborated by TP-XPS of C 1s core levels. These insights are anticipated to play an important role regarding our ability to rationally synthesize atomically precise low-dimensional covalent nanostructures on surfaces.

Competitive Metal Coordination of Hexaaminotriphenylene on Cu(111) by Intrinsic Copper Versus Extrinsic Nickel Adatoms.

The interplay between the self-assembly and surface chemistry of 2,3,6,7,10,11-hexaaminotriphenylene (HATP) on Cu(111) was complementarily studied by high-resolution scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) under ultra-high vacuum conditions. To shed light on the competitive metal coordination, comparative experiments were carried out on pristine and nickel-covered Cu(111). Directly after room-temperature deposition of HATP onto pristine Cu(111), self-assembled aggregates were observed by STM, and XPS results indicated still protonated amino groups. Annealing up to 200 °C activated the progressive single deprotonation of all amino groups as indicated by chemical shifts of both the N 1s and C 1s core levels in the XP spectra. This enabled the formation of topologically diverse π-d conjugated coordination networks with intrinsic copper adatoms. The basic motif of these networks was a metal-organic trimer, in which three HATP molecules were coordinated by Cu3 clusters, as corroborated by the accompanying density functional theory (DFT) simulations. Additional deposition of more reactive nickel atoms resulted in both chemical and structural changes with deprotonation and formation of bis(diimino)-Ni bonded networks already at room temperature. Even though fused hexagonal metal-coordinated pores were observed, extended honeycomb networks remained elusive, as tentatively explained by the restricted reversibility of these metal-organic bonds.

What can be inferred from moiré patterns? A case study of trimesic acid monolayers on graphite.

Self-assembly of benzene-1,3,5-tricarboxylic acid (trimesic acid - TMA) monolayers at the alkanoic acid-graphite interface is revisited. Even though this archetypal model system for hydrogen bonded porous networks is particularly well studied, the analysis of routinely observed superperiodic contrast modulations known as moiré patterns lags significantly behind. Fundamental questions remain unanswered such as, are moiré periodicity and orientation always the same, i.e. is exclusively only one specific moiré pattern observed? What are the geometric relationships (superstructure matrices) between moiré, TMA, and graphite lattices? What affects the moiré pattern formation? Is there any influence from solvent, concentration, or thermal treatment? These basic questions are addressed via scanning tunneling microscopy experiments at the liquid-solid interface, revealing a variety of different moiré patterns. Interestingly, TMA and graphite lattices were always found to be ∼5° rotated with respect to each other. Consequently, the observed variation in the moiré patterns is attributed to minute deviations (<2°) from this preferred orientation. Quantitative analysis of moiré periods and orientations facilitates the determination of the TMA lattice parameter with picometer precision.

Post-Synthetic Decoupling of On-Surface-Synthesized Covalent Nanostructures from Ag(111).

The on-surface synthesis of covalent organic nanosheets driven by reactive metal surfaces leads to strongly adsorbed organic nanostructures, which conceals their intrinsic properties. Hence, reducing the electronic coupling between the organic networks and commonly used metal surfaces is an important step towards characterization of the true material. We demonstrate that post-synthetic exposure to iodine vapor leads to the intercalation of an iodine monolayer between covalent polyphenylene networks and Ag(111) surfaces. The experimentally observed changes from surface-bound to detached nanosheets are reproduced by DFT simulations. These findings suggest that the intercalation of iodine provides a material that shows geometric and electronic properties substantially closer to those of the freestanding network.

Iodine passivation facilitates on-surface synthesis of robust regular conjugated two-dimensional organogold networks on Au(111).

Two-dimensional conjugated organogold networks with anthra-tetrathiophene repeat units are synthesized by thermally activated debrominative coupling of 2,5,9,12-tetrabromoanthra[1,2-b:4,3-b':5,6-b'':8,7-b''']tetrathiophene (TBATT) precursor molecules on Au(111) surfaces under ultra-high vacuum (UHV) conditions. Performing the reaction on iodine-passivated Au(111) surfaces promotes formation of highly regular structures, as revealed by scanning tunneling microscopy (STM). In contrast, coupling on bare Au(111) surfaces results in less regular networks due to the simultaneous expression of competing intermolecular binding motifs in the absence of error correction. The carbon-Au-carbon bonds confer remarkable robustness to the organogold networks, as evidenced by their high thermal stability. In addition, as suggested by density functional theory (DFT) calculations and underscored by scanning tunneling spectroscopy (STS), the organogold networks exhibit a small electronic band gap in the order of 1.0 eV due to their high π-conjugation.

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.

Born-Haber cycle for monolayer self-assembly at the liquid-solid interface: assessing the enthalpic driving force.

The driving force for self-assembly is the associated gain in free energy with decisive contributions from both enthalpy and entropy differences between final and initial state. For monolayer self-assembly at the liquid-solid interface, solute molecules are initially dissolved in the liquid phase and then become incorporated into an adsorbed monolayer. In this work, we present an adapted Born-Haber cycle for obtaining precise enthalpy values for self-assembly at the liquid-solid interface, a key ingredient for a profound thermodynamic understanding of this process. By choosing terephthalic acid as a model system, it is demonstrated that all required enthalpy differences between well-defined reference states can be independently and consistently assessed by both experimental and theoretical methods, giving in the end a reliable value of the overall enthalpy gain for self-assembly of interfacial monolayers. A quantitative comparison of enthalpy gain and entropy cost reveals essential contributions from solvation and dewetting, which lower the entropic cost and render monolayer self-assembly a thermodynamically favored process.

Control of intermolecular bonds by deposition rates at room temperature: hydrogen bonds versus metal coordination in trinitrile monolayers.

Self-assembled monolayers of 1,3,5-tris(4'-biphenyl-4"-carbonitrile)benzene, a large functional trinitrile molecule, on the (111) surfaces of copper and silver under ultrahigh vacuum conditions were studied by scanning tunneling microscopy and low-energy electron diffraction. A densely packed hydrogen-bonded polymorph was equally observed on both surfaces. Additionally, deposition onto Cu(111) yielded a well-ordered metal-coordinated porous polymorph that coexisted with the hydrogen-bonded structure. The required coordination centers were supplied by the adatom gas of the Cu(111) surface. On Ag(111), however, the well-ordered metal-coordinated network was not observed. Differences between the adatom reactivities on copper and silver and the resulting bond strengths of the respective coordination bonds are held responsible for this substrate dependence. By utilizing ultralow deposition rates, we demonstrate that on Cu(111) the adatom kinetics plays a decisive role in the expression of intermolecular bonds and hence structure selection.

Adsorption structure determination of a large polyaromatic trithiolate on Cu(111): combination of LEED-I(V) and DFT-vdW.

The adsorption geometry of 1,3,5-tris(4-mercaptophenyl)benzene (TMB) on Cu(111) is determined with high precision using two independent methods, experimentally by quantitative low energy electron diffraction (LEED-I(V)) and theoretically by dispersion corrected density functional theory (DFT-vdW). Structural refinement using both methods consistently results in similar adsorption sites and geometries. Thereby a level of confidence is reached that allows deduction of subtle structural details such as molecular deformations or relaxations of copper substrate atoms.

Creating a foundation for origin of life outreach: How scientists relate to their field, the public, and religion.

Origins of life research is particularly challenging to communicate because of the tension between its many disciplines and its nearness to traditionally philosophical or religious questions. To authentically represent scientists' perspective in a museum exhibition, we interviewed 46 researchers from diverse backgrounds. We investigated how they perceive their field, science communication, and the relation with religion. Results show that researchers actively participate in resolving the scientific debate, but delegate the resolution of controversies involving non-scientific institutions. Advocating for science is the foremost communication goal in all contexts. Career stage, research subject, religiosity, etc. influence the approach to controversies and communication.

Incorporation dynamics of molecular guests into two-dimensional supramolecular host networks at the liquid-solid interface.

The objective of this work is to study both the dynamics and mechanisms of guest incorporation into the pores of 2D supramolecular host networks at the liquid-solid interface. This was accomplished by adding molecular guests to prefabricated self-assembled porous monolayers and the simultaneous acquisition of scanning tunneling microscopy (STM) topographs. The incorporation of the same guest molecule (coronene) into two different host networks was compared, where the pores of the networks either featured a perfect geometric match with the guest (for trimesic acid host networks) or were substantially larger than the guest species (for benzenetribenzoic acid host networks). Even the moderate temporal resolution of standard STM experiments in combination with a novel injection system was sufficient to reveal clear differences in the incorporation dynamics in the two different host networks. Further experiments were aimed at identifying a possible solvent influence. The interpretation of the results is aided by molecular mechanics (MM) and molecular dynamics (MD) simulations.

On-surface photopolymerization of two-dimensional polymers ordered on the mesoscale.

The use of solid supports and ultra-high vacuum conditions for the synthesis of two-dimensional polymers is attractive, as it can enable thorough characterization, often with submolecular resolution, and prevent contamination. However, most on-surface polymerizations are thermally activated, which often leads to high defect densities and relatively small domain sizes. Here, we have obtained a porous two-dimensional polymer that is ordered on the mesoscale by the two-staged topochemical photopolymerization of fluorinated anthracene triptycene (fantrip) monomers on alkane-passivated graphite surfaces under ultra-high vacuum. First, the fantrip monomers self-assemble into highly ordered monolayer structures, where all anthracene moieties adopt a suitable arrangement for photopolymerization. Irradiation with violet light then induces complete covalent crosslinking by [4+4] photocycloaddition to form a two-dimensional polymer, while fully preserving the long-range order of the self-assembled structure. The extent of the polymerization is confirmed by local infrared spectroscopy and scanning tunnelling microscopy characterization, in agreement with density functional theory calculations, which also gives mechanistic insights.

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.

Inhibition of Toll-like receptors TLR4 and 7 signaling pathways by SIGIRR: a computational approach.

Toll-like receptors (TLRs) belong to the Toll-like receptor/interleukin-1 receptor (TLR/IL-1R) superfamily which is defined by a common cytoplasmic Toll/interleukin-1 receptor (TIR) domain. TLRs recognize pathogen-associated molecular patterns and initiate an intracellular kinase cascade to trigger an immediate defensive response. SIGIRR (single immunoglobulin interleukin-1 receptor-related molecule), another member of the TLR/IL-1R superfamily, acts as a negative regulator of MyD88-dependent TLR signaling. It attenuates the recruitment of MyD88 adaptors to the receptors with its intracellular TIR domain. Thus, SIGIRR is a highly important molecule for the therapy of autoimmune diseases caused by TLRs. So far, the structural mechanism of interactions between SIGIRR, TLRs and adaptor molecules is unclear. To develop a working hypothesis for this interaction, we constructed three-dimensional models for the TIR domains of TLR4, TLR7, MyD88 and SIGIRR based on computational modeling. Through protein-protein docking analysis, we developed models of essential complexes involved in the TLR4 and 7 signaling and the SIGIRR inhibiting processes. We suggest that SIGIRR may exert its inhibitory effect through blocking the molecular interface of TLR4, TLR7 and the MyD88 adaptor mainly via its BB-loop region.

Reversible phase transitions in self-assembled monolayers at the liquid-solid interface: temperature-controlled opening and closing of nanopores.

We present a variable-temperature study of monolayer self-assembly at the liquid-solid interface. By means of in situ scanning tunneling microscopy (STM), reversible phase transitions from a nanoporous low-temperature phase to a more densely packed high-temperature phase are observed. The occurrence of the phase transition and the respective transition temperature were found to depend on the type of solvent and solute concentration. Estimates of the entropic cost and enthalpic gain upon monolayer self-assembly suggest that coadsorption of solvent molecules within the cavities of the nanoporous structure renders this polymorph thermodynamically stable at low temperatures. At elevated temperatures, however, desorption of these relatively weakly bound solvent molecules destabilizes the nanoporous polymorph, and the densely packed polymorph becomes thermodynamically favored. Interestingly, the structural phase transition provides external control over the monolayer morphology and, for the system under discussion, results in an effective opening and closing of supramolecular nanopores in a two-dimensional molecular monolayer.

Nanostructure and mechanics of mummified type I collagen from the 5300-year-old Tyrolean Iceman.

Skin protects the body from pathogens and degradation. Mummified skin in particular is extremely resistant to decomposition. External influences or the action of micro-organisms, however, can degrade the connective tissue and lay the subjacent tissue open. To determine the degree of tissue preservation in mummified human skin and, in particular, the reason for its durability, we investigated the structural integrity of its main protein, type I collagen. We extracted samples from the Neolithic glacier mummy known as 'the Iceman'. Atomic force microscopy (AFM) revealed collagen fibrils that had characteristic banding patterns of 69 +/- 5 nm periodicity. Both the microstructure and the ultrastructure of dermal collagen bundles and fibrils were largely unaltered and extremely well preserved by the natural conservation process. Raman spectra of the ancient collagen indicated that there were no significant modifications in the molecular structure. However, AFM nanoindentation measurements showed slight changes in the mechanical behaviour of the fibrils. Young's modulus of single mummified fibrils was 4.1 +/- 1.1 GPa, whereas the elasticity of recent collagen averages 3.2 +/- 1.0 GPa. The excellent preservation of the collagen indicates that dehydration owing to freeze-drying of the collagen is the main process in mummification and that the influence of the degradation processes can be addressed, even after 5300 years.

On the scalability of supramolecular networks--high packing density vs optimized hydrogen bonds in tricarboxylic acid monolayers.

We present a scanning tunneling microscopy (STM) based study of 1,3,5-tris[4'-carboxy(1,1'-biphenyl-4-yl)]benzene (TCBPB) monolayers at the liquid-solid interface. In analogy to smaller aromatic 3-fold symmetric tricarboxylic acids, this compound was aimed to yield two-dimensional nanoporous networks with large cavities. Depending on the solute concentration, three crystallographically distinct phases with pores of different size and shape were observed on graphite (001) with heptanoic acid as solvent. All three phases have the same dimer motif as basic building block in common. Yet, as opposed to other carboxylic acid assemblies, these dimers are not interconnected by 2-fold O-H...O hydrogen bonds as anticipated, but by two energetically inferior C-H...O hydrogen bonds. Instead of the common head-to-head arrangement, this bonding pattern results in displaced dimers, which allow for higher packing density, and due to their lower symmetry give rise to chiral polymorphs. In accordance with studies of comparable systems, a positive correlation between solute concentration and average surface packing density is identified and rationalized by thermodynamic arguments.

Quantifying the Ultraslow Desorption Kinetics of 2,6-Naphthalenedicarboxylic Acid Monolayers at Liquid-Solid Interfaces.

Kinetic effects in monolayer self-assembly at liquid-solid interfaces are not well explored but can provide unique insights. We use variable-temperature scanning tunneling microscopy (STM) to quantify the desorption kinetics of 2,6-naphthalenedicarboxylic acid (NDA) monolayers at nonanoic acid-graphite interfaces. Quantitative tracking of the decline of molecular coverages by STM between 57.5 and 65.0 °C unveiled single-exponential decays over the course of days. An Arrhenius plot of rate constants derived from fits results in a surprisingly high energy barrier of 208 kJ mol-1 that strongly contrasts with the desorption energy of 16.4 kJ mol-1 with respect to solution as determined from a Born-Haber cycle. This vast discrepancy indicates a high-energy transition state. Expanding these studies to further systems is the key to pinpointing the molecular origin of the remarkably large NDA desorption barrier.

Aromatic interaction vs. hydrogen bonding in self-assembly at the liquid-solid interface.

Interfacial self-assembly of specific monolayer structures from solution on a graphite surface can be steered by tuning the interplay between solute-solute and solute-solvent interactions.