Hydrogen and coordination bonding supramolecular structures of trimesic acid on Cu(110)

The adsorption of trimesic acid (TMA) on Cu(110) has been studied in the temperature range between 130 and 550 K and for coverages up to one monolayer. We combine scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), reflection absorption infrared spectroscopy (RAIRS), X-ray photoemission spectroscopy (XPS), and density functional theory (DFT) calculations to produce a detailed adsorption phase diagram for the TMA/Cu(110) system as a function of the molecular coverage and the substrate temperature. We identify a quite complex set of adsorption phases, which are determined by the interplay between the extent of deprotonation, the intermolecular bonding, and the overall energy minimization. For temperatures up to 280 K, TMA molecules are only partly deprotonated and form hydrogen-bonded structures, which locally exhibit organizational chirality. Above this threshold, the molecules deprotonate completely and form supramolecular metal-organic structures with Cu substrate adatoms. These structures exist in the form of single and double coordination chains, with the molecular coverage driving distinct phase transitions.

Chiral recognition and supramolecular self-assembly of adsorbed amino acids and dipeptides at the submolecular level

Magalí Alejandra Lingenfelder

This thesis deals with the supramolecular organization of chiral aminoacids and dipeptides on metal surfaces. The emergence of homochirality in biomolecular systems is one of the most intriguing open questions of Nature. The self-assembly and amplification of chiral subunits into higher-order species is crucial in understanding the development of homochirality in biological function. Apart from being related to the very first organic molecules synthesized on earth, understanding the basics of chiral recognition and discrimination is of high technological relevance. In fact, the chemistry and technology of production and separation of enantiomers has evolved into a branch of materials science under the name of Chirotechnology. Even before the concept of molecule existed, Pasteur pointed out that the asymmetry of the crystals of tartaric acid he observed was related to the asymmetry of the components of which they were made. Nowadays, we can asses the landscape of these components even at the submolecular level by means of Scanning Tunneling Microscopy (STM). The aim of this thesis is twofold: primary to get an insight into the fundamental aspects of chiral recognition, under the main inspiring question: How does chiral recognition take place at the single molecule level? and secondly: How can we tune the expression of chirality on a metal surface to achieve global templation? The first part of this thesis presents a comprehensive study of the basic requirements for amino acid chiral templation of metal surfaces. By comparatively studying the adsorption behaviour of L-Phenylalanine (L-Phe) and L-Tyrosine (L-Tyr) on Cu(110) we show that conformational rigidity is a key parameter for the expression of footprint homochirality on metal surfaces. This parameter can be tuned by the appropriate choice of the amino acid residue. The molecular structure of the adsorbed molecules is studied by a combination of reflection absorption infrared spectroscopy (RAIRS), STM and molecular dynamics simulations (MD). The second part of the thesis focuses on the transfer of molecular chirality to supramolecular structures of Di-Phenylalanine (Phe-Phe) on Cu(110). We have followed the chiral recognition and discrimination among individual Phe-Phe enantiomers by STM and rationalized it using first principles and classical molecular dynamics simulations. The geometrical parameters of the final supramolecular structures are studied by near edge absorption fine structure (NEXAFS). Our results show that molecules whose static structure is not optimized for specific binding can selectively recognize each other and link through mutually induced conformational changes. The general idea of induced molecular fit in biomolecular recognition was introduced by Linus Pauling more than 50 years ago. We now report direct evidence of this dynamic scenario at the single molecule level. The last part of this thesis deals with the adsorption phase diagram of Phe-Phe on Cu(110). The encountered adsorption motifs and the chemical processes involved in the phase transitions are investigated by a combination of STM, X-ray photoelectron spectroscopy (XPS), low energy electron diffraction (LEED) and thermal programme desorption (TPD). The resulting supramolecular assemblies expose chiral cavities that can potentially be used as enantioselective adsorption sites.

EPFL2008

Two-dimensional metal-organic coordination networks of Mn-7,7,8,8-tetracyanoquinodimethane assembled on Cu(100): Structural, electronic, and magnetic properties

Klaus Kern, Tzu-Chun Tseng

A compound two-dimensional (2D) monolayer mixing Mn atoms and 7,7,8,8-tetracyanoquinodimethane (TCNQ) molecules was synthesized by supramolecular assembly on a Cu(100) surface under ultrahigh vacuum conditions. Its structural, electronic, and magnetic properties were analyzed by scanning tunneling microscopy experiment and theory, low-energy electron diffraction, x-ray photoemission spectroscopy, and density-functional theory calculations. The 2D compound has a long-range ordered square planar network structure consisting of fourfold coordinated Mn centers with a Mn: TCNQ ratio of 1:2. The electronic-state analysis revealed a complex charge-transfer scenario indicating strong bonding of TCNQ with both the Mn adsorbates and the Cu surface atoms. The calculations reveal that the Mn centers carry a magnetic moment close to 5 mu(B) with very weak coupling between adjacent Mn centers.

2009

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.