Supramolecular Self-Assembly Driven by Electrostatic Repulsion: The 1D Aggregation of Rubrene Pentagons on Au(111)

At present, organic molecules are among the best candidate "building blocks" for the construction of self-assembling nanoscale devices based on metal substrates. Control of the formation of specific patterns In the submonolayer regime is usually achieved by appropriate choice and/or functionalization of the adsorbates. The effect of this intervention, though, is limited by the typically short-range character of the bonding. We present here a theoretical study on the system rubrene/gold to show that substrate-induced molecular charging can Instead determine the assembly on larger scales. OFT calculations and electrostatic considerations are used to discuss the charge transfer at the metal/organic Interface. This allows rationalization of previous puzzling experimental results and, in particular, of the unusual molecular gap broadening upon adsorption observed in STS spectra. The self-assembly process is further studied by means of classical molecular dynamics simulations. The charged adsorbates are modeled as mutually repulsive standing dipoles, with van der Waals interactions Intervening at short distances. The striking resemblance between the experimental STM images and the results of our MD simulations shows that this simple model is able to capture the key effects driving the assembly in this system. The competition between long-range repulsive Interactions and short-range attractive forces leads to characteristic and easily recognizable 1D patterns. We suggest that experimental evidence of the presence of similar patterns in other meta/organic systems can provide crucial information on the electronic level alignment at the interface, that is, on the occurrence of charge-transfer processes between metal and organic adsorbates.

Design of Surface-Supported Bio-inspired Networks for CO2 and O2 Activation at Room Temperature

Daniel Eduardo Hurtado Salinas

The structure of a biological system defines its function. Therefore, nature has developed sophisticated systems that catalyze chemical reactions that are vital for life on earth. For instance, the photosynthesis is a biological process that is partially regulated by the metallo-enzyme RuBisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase), whose function is to catalyze the capture and transfer of CO2 into organic molecules. This carboxylation reaction occurs at the active site, where a magnesium ion (Mg2+) is bound to organic molecules with carboxylate (COO-) and amine (NH2) functional groups. In the last decades, supramolecular chemistry has proven to be a valid approach to replicate the structural characteristics of these natural metal-organic systems. Metal atoms and organic molecules are used as building blocks to form two-dimensional (2D) metal-organic networks (MONs) on metal surfaces, through a self-assembly process that occurs spontaneously. In these systems the molecules bind to the metal centers and control their oxidation states that, as found in metallo-enzymes, is crucial to perform a catalytic task. Therefore, these supramolecular assemblies show promising features to be explored for heterogeneous catalysis. The main objective of this thesis is to reverse the structure-function equation, that is: instead of finding specific functions of well-known 2D structures for future applications, 2D structures are designed to reproduce the specific functions of well-known bio-systems. Thus, inspired in the structure of the active site of RuBisCO, 2D Mg-based supramolecular assemblies are rationally designed on Cu(100) or Mg(0001) surfaces at room temperature (RT) as a platform for CO2 adsorption. This work is the first study of self-assembly of alkaline earth metal atoms (Mg) with organic molecules ((1,4-benzenedicarboxylic acid (TPA) and 2,4,6-tris(4-aminophenyl)-1,3,5-triazine (TAPT)) on metal surfaces. The first part of this thesis investigates the self-assembly of TAPT molecules. Scanning Tunneling Microscopy (STM) and High Resolution X-ray Photoemission Spectroscopy (HR-XPS) demonstrate that the molecules typically semi-deprotonate to form MONs with the adatoms from the host substrates. The exposure of these structures to CO2 results in the carboxylation of the amino groups. The second part proves that the COOH moieties of TPA molecules fully-deprotonate to form homo-molecular structures. The incorporation of Mg adatoms result in ionic MONs, which reproduce the carboxylate environment of the active site of RuBiSCO. STM, XPS and Density Functional Theory (DFT) analyze the structural changes, the chemical reactions and charge transfer during either the CO2 or O2 adsorption on the Mg2+ centers. The last part focusses on the co-deposition of both molecules to form 2D metallic-hetero-molecular networks with Mg2+ centers. The role of the Mg2+ centers as active sites for molecular adsorption and model systems for gas storage is studied. STM reveals that CO2 partially modifies the network towards a configuration that resembles the active site of RuBisCO. The formation of 3D structures to enhance CO2 adsorption is also evaluated.

EPFL2018

Single-molecule-level characterization of supramolecular systems at surfaces

Dietmar Payer

This thesis deals with the self-organization of individual building blocks, specifically organic molecules and metal atoms, into supramolecular structures on metal surfaces under ultra high vacuum conditions (UHV). Self-organization of supramolecular systems is a promising candidate for a bottom-up approach in the fabrication of complex structures with specific properties. This process is steered by interactions between functional groups of the individual building blocks and is of apparent interest to gain a detailed understanding of the influence and the behavior of these functional groups enabling intermolecular binding. In the first part of the thesis, we investigate hydrogen bonded structures on metal surfaces. Of especial interest is the possibility of the formation of ionic hydrogen bonds, a special class of hydrogen bond which connects a charged donor (acceptor) and a neutral acceptor (donor) and is important in biological systems. By combined Scanning Tunneling Microscopy (STM), X-ray Photoelectron Spectroscopy (XPS) and Near Edge X-ray Absorption Fine Structure (NEXAFS) measurement we show the deprotonation of carboxylic functions in the molecules, forming carboxylate groups involved in intermolecular binding. With our complementary experimental and theoretical examinations we clearly show that the carboxylate groups are indeed still charged although adsorbed onto a conducting metal surface and that the observed structures can be computationally reproduced by using these charges in classical molecular dynamic calculations. Our investigations clearly reveal that all requirements for the formation of ionic hydrogen bonds in these samples at metal surfaces under solvent free conditions are fulfilled. In the second part, the confinement of surface state electrons in self-assembled hydrogen-bonded structures is investigated. The examined structure contains two-dimensional cavities, with different inner diameters in the periodic arrangement and in domain boundaries. Inside the cavities we detect a spatially localized modification in the local density of states (LDOS) of the Ag(111) surface state electrons. The energy of the peak correlates with the cavity area as predicted by a simple "particle in a box" model. This clearly shows that the surface state electrons form a confined state inside the cavities. Furthermore we examine self-assembled periodic structures as templates for binding single macrocyclic molecules. The macrocyclic molecules can be deposited by sublimation, as STM-topographs with submolecular resolution reflect the shape of the intact molecules and reveal a coverage dependent aggregation behavior. We show that it is possible to fabricate a structure in which at most one macrocyclic molecule per pore can be found in a defined binding position. In the last part of the thesis we investigate the influence of individual metal atoms on the chemical activity and the self-assembly process of molecules on metal surfaces. First, we demonstrate the high chemical reactivity of these metal atoms. In our experiments we address the chemical reactivity of static active sites, like kinks and step edges, and of dynamic active sites, like the metal atoms, separately. Doing this we show that a non-negligible amount of the chemical reactivity of a metal surface is due to this dynamic adatom gas. Furthermore the influence of metal atoms on the structure formation of organic molecules is investigated. We show that two-dimensional structures based on a complex formation between metal centers and ligands can be formed and that the coordination number is independent of the substrate symmetry. Furthermore, we show the possibility that on metal surfaces one can prepare three-fold coordinated Fe-centers, a coordination number which is rarely seen in three dimensional chemistry. In the last part we study catenanes, which consist of two interlocked macrocyclic molecules. Main interest is on the confirmation of a structural change of the catenanes adsorbed on a metal substrate. For our experiments we use the fact that the catenanes are designed to "trap" a Cu-atom by complex formation. As this reaction is associated with a structural change and a change in intermolecular interaction, we can verify a reaction of catenanes adsorbed onto a surface with Cu adatoms and therefore a structural alteration by simply imaging the formed structures. Our measurements show the possibility of depositing large molecules like catenanes by sublimation and of their potential for use as molecular machines adsorbed onto metal surfaces.

EPFL2007

Dynamics of nanoscale systems probed by time-resolved STM-induced luminescence

Anna Maria Roslawska

The efficiency and peculiarities of processes such as surface adsorption or electron-to-photon energy conversion in organic and inorganic structures are determined by the dynamics at the scale of individual molecules, atoms and charges. The timescales of such effects reach down to the ps regime, which can be routinely probed using ultrafast optics methods. However, these far-field techniques suffer from ensemble-averaging that obscures the information encoded at the atomic level. These limits can be overcome by combining scanning tunnelling microscopy (STM) with time-resolved light detection so that pm and ps scales can be reached simultaneously. STM-induced luminescence (STML) methodologies are employed in this thesis to explore the nanoscale dynamics of different systems: light emitting defects in C60 thin films, H2 molecules weakly physisorbed on Au(111), metal-metal tunnel junctions and single atom contacts. First, we study the dynamics associated with the radiative decay of single excitons at defect-related emission centres localized in the C60 molecular film. Such emission centres serve as the smallest possible model of an organic light emitting diode where a single electron and hole recombine producing a photon. Using time-resolved STML (TR-STML) excited by voltage pulses, we follow the formation of an individual exciton and map this process in real space with ns resolution. Besides the excitonic emission, on C60 thin films we observe luminescence due to the radiative decay of plasmons. We study the interplay of these two processes and create a nanoscale bimodal source whose emission can be dynamically tuned by controlling the charge injection rate. A kinetic model is employed to thoroughly describe the charge and exciton dynamics in this system. The developed kinetic model can be also used to analyse the motion of hydrogen molecules adsorbed on an Au(111) crystal. The weak interaction with the metal and the continuous charge injection by the tip leads to recurrent excursions of the molecule inside and outside from the tunnelling junction, which chop the plasmonic luminescence intensity. These dynamical changes in the light intensity can be followed by correlation spectroscopy and allow extraction of the molecule's residence and excursion times. In the next step, we probe the dynamics of a generic metal-metal tunnel junction. Interestingly, when a high bias is applied, the emission from the junction exhibits photon bunching on a time scale below 50 ps as evidenced by Hanbury Brown-Twiss interferometry. Such a process is a result of a distribution of the energy of one electron between two photons, which may possibly be entangled. The opposite process may occur as well, under conditions where two electrons interact supplying energy to one photon. This overbias emission is a feature of single atom contacts and is used here to probe the fluctuations of plasmonic enhancement driven by the motion of single atoms in the vicinity of such a contact.

EPFL2019