Coexistence of one- and two-dimensional supramolecular assemblies of terephthalic acid on Pd(111) due to self-limiting deprotonation

The adsorption of terephthalic acid [C6H4(COOH)(2), TPA] on a Pd(111) surface has been investigated by means of scanning tunneling microscopy (STM), x-ray photoelectron spectroscopy, and near-edge x-ray absorption fine structure spectroscopy under ultrahigh vacuum conditions at room temperature. We find the coexistence of one- (1D) and two-dimensional (2D) molecular ordering. Our analysis indicates that the 1D phase consists of intact TPA chains stabilized by a dimerization of the self-complementary carboxyl groups, whereas in the 2D phase, consisting of deprotonated entities, the molecules form lateral ionic hydrogen bonds. The supramolecular growth dynamics and the resulting structures are explained by a self-limiting deprotonation process mediated by the catalytic activity of the Pd surface. Our models for the molecular ordering are supported by molecular mechanics calculations and a simulation of high resolution STM images.

Growth and characterization of specific self-assembled supramolecular architectures at crystal surfaces

Marta Canas Ventura

In the framework of this thesis self-assembled supramolecular architectures of several molecular species on crystal metal surfaces are characterized. These investigations combine results obtained by means of scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), X-Ray Photoelectron Spectroscopy (XPS), and Near-Edge X-Ray Absorption Fine Structure Spectroscopy (NEXAFS). The interest in controlling the formation of specific arrangements of supramolecular ensembles at surfaces is motivated to a great extent by the prospect to design molecular devices and nanomaterials with customized properties. The goal is a "spontaneous" creation of targeted, well-ordered molecular architectures, which shall be achieved by taking advantage of the molecule's propensity to self-assemble. Control means, in this context, predictability. This term address the accuracy of the prediction of the structures resulting from molecular self-assembly for systems exhibiting different characteristics. Here, system stands for a particular combination of a single-crystal surface and adsorbed molecular species. In a first part, the focus is given to the impact of a Pd(111) surface exhibiting high chemical activity. Due to surface induced deprotonation two resulting chemical states are found for the adsorbed terephthalic acid species. Deprotonation of the carboxyl moieties is observed to affect the topology of the molecular assemblies even though hydrogen bonds (H-bonds) are responsible for the stabilization of assemblies of both, intact and deprotonated molecular species. Therefore, the selective fabrication of a single specific molecular structure becomes a challenge when the surface is prone to induce chemical reactions. Secondly, a molecular species exhibiting conformational flexibility is studied on a largely inert Au(111) surface. It is observed that the characteristic conformational flexibility is also active on the surface, and the molecule is found to adopt different conformations depending on the locally most favorable bonding motif. In particular, phenyl groups may undergo a rotation such that one-dimensional chains can be stabilized by means of intermolecular H-bonds. This phenomenon is very interesting from an adsorbate-substrate interaction point of view, but it limits the predictability of supramolecular structures formed upon self-assembly. In a third step, a comparative study of the self-assembly of three closely related molecular species highlights the impact of concurrent competing intermolecular interactions. Molecules exhibiting an increasing number of possible interaction channels are found to assemble into an increasing number of distinct supramolecular architectures. The most flexible molecular species allowing for different hydrogen-bonding patterns as well as dipolar coupling self-assembles into various structurally complex architectures. Structural predictability, however, is low since the formation of one or the other assembly appears to depend on small variations in sample preparation conditions and on poorly controllable local surface properties. Finally, a system where the resulting structures fully agree with predictions evidences the possibility to control the formation of targeted specific supramolecular architectures. The formation of well ordered bimolecular ribbons and wires over extended length scales is accomplished by the rational choice of both, complementary building blocks for the selective formation of three-fold H-bonds and a nanostructured surface to guide the molecular self-assembly. Furthermore, the impact of H-bond formation on the electronic structure of self-assembled molecular building blocks is probed by STS measurements. The experimental data reveal shifts in the electronic levels depending on the H-bond configuration and on the local characteristics of the underlying surface. In order to improve the precision of such a study, single molecules, homo- and heteromolecular dimers as well as trimers are successfully isolated and assembled by molecular manipulation with the STM tip. Further STS studies on such artificially assembled structures are suggested.

EPFL2008

STM study of terephthalic acid self-assembly on Au(III): Hydrogen-bonded sheets on an inhomogeneous substrate

Harald Brune, Sylvain Clair, Klaus Kern

The adsorption and ordering of the molecule terephthalic acid (TPA), 1,4-benzene-dicarboxylic acid C6H4-(COOH)(2), on the reconstructed Au(111) surface has been studied in situ in ultrahigh vacuum by scanning tunneling microscopy (STM) at room temperature. Two-dimensional (2D) self-assembled supramolecular domains evolve, wherein the well-known one-dimensional (1D) carboxyl H-bond pairing scheme is identified. Since the individual molecules occupy a distinct adsorption site and the supramolecular ordering usually extends over several substrate reconstruction domains, a significant variation in hydrogen bond lengths is encountered, which illustrates the versatility of hydrogen bridges in molecular engineering at surfaces. Ab initio calculations for a 1D H-bonded molecular chain provide insight into the limited geometric response of the molecules in different local environments.

American Chemical Society2004

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.