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

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.

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

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

Daniel Eduardo Hurtado Salinas

EPFL2018

Single-molecule-level characterization of supramolecular systems at surfaces

Dietmar Payer

EPFL2007