Short-Range Structural Correlations in Amorphous 2D Polymers

Many 2D covalent polymers synthesized as single layers on surfaces show inherent disorder, expressed for example in their ring-size distribution. Systems which are expected to form the thermodynamically favored hexagonal lattice usually deviate from crystallinity and include high numbers of pentagons, heptagons, and rings of other sizes. The amorphous structure of two different covalent polymers in real space using scanning tunneling microscopy is investigated. Molecular dynamics simulations are employed to extract additional information. We show that short-range correlations exist in the structure of one polymer, i. e. that polygons are not tessellating the surface randomly but that ring neighborhoods have preferential compositions. The correlation is dictated by the energy of formation of the ring neighborhoods.

Interplay of Chemical and Electronic Structure on the Single-Molecule Level in 2D Polymerization

Klaus Kern, Claudius Morchutt, Carola Strasser

Single layers of covalently linked organic materials in the form of two-dimensional (2D) polymers constitute structures complementary to inorganic 2D materials. The electronic properties of 2D polymers may be manipulated through a deliberate choice of the organic precursors. Here we address the changes in electronic CO structure-from precursor molecule to oligomer by scanning tunneling spectroscopy and ultraviolet photoelectron spectroscopy. For this purpose, we introduce the polymerization reaction of 1,3,5-tris(4-carboxyphenyl)benzene via decarboxylation on Cu(111), which is thoroughly characterized by scanning tunneling microscopy, X-ray photoelectron spectroscopy, and density functional theory calculations. We present a comprehensive study of a contamination-free on-surface coupling scheme and study how dehydrogenation, decarboxylation, and polymerization affect the electronic structure on the molecular level.

American Chemical Society2016

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

Structure determination of an amorphous drug through large-scale NMR predictions

Martins Balodis, Pierrick Berruyer, Manuel Cordova, David Lyndon Emsley, Albert Hofstetter, Federico Maria Paruzzo, Bruno Simões de Almeida

Knowledge of the structure of amorphous solids can direct, for example, the optimization of pharmaceutical formulations, but atomic-level structure determination in amorphous molecular solids has so far not been possible. Solid-state nuclear magnetic resonance (NMR) is among the most popular methods to characterize amorphous materials, and molecular dynamics (MD) simulations can help describe the structure of disordered materials. However, directly relating MD to NMR experiments in molecular solids has been out of reach until now because of the large size of these simulations. Here, using a machine learning model of chemical shifts, we determine the atomic-level structure of the hydrated amorphous drug AZD5718 by combining dynamic nuclear polarization-enhanced solid-state NMR experiments with predicted chemical shifts for MD simulations of large systems. From these amorphous structures we then identify H-bonding motifs and relate them to local intermolecular complex formation energies. Determining the structure of amorphous solids is important for optimization of pharmaceutical formulations, but direct relation of molecular dynamics (MD) simulations and NMR to achieve this is challenging. Here, the authors use a machine learning model of chemical shifts to solve the atomic-level structure of the hydrated amorphous drug AZD5718 by combining dynamic nuclear polarization-enhanced solid-state NMR with predicted shifts for MD simulations of large systems.

NATURE RESEARCH2021

Single-molecule-level characterization of supramolecular systems at surfaces

Dietmar Payer

EPFL2007