Two-Dimensional Folding of Polypeptides into Molecular Nanostructures at Surfaces

Herein we report the fabrication of molecular nanostructures on surfaces via two-dimensional (2D) folding of the nine amino acid peptide bradykinin. Soft-landing electrospray ion beam deposition in conjunction with high-resolution imaging by scanning tunneling microscopy is used to fabricate and investigate the molecular nanostructures. Subnanometer resolved images evidence the large conformational freedom of the molecules if thermal motion is inhibited and the formation of stable uniform dimers of only one specific conformation when diffusion can take place. Molecular dynamics modeling supported by density functional theory calculations give atomically precise insight into the induced-fit binding scheme when the folded dimer is formed. In the absence of solvent, we find a hierarchy of binding strength from polar to nonpolar, manifested in an inverted polar nonpolar segregation which suppresses unspecific interactions at the rim of the nanostructure. The demonstrated 2D-folding scheme resembles many key properties of its native 3D counterpart and shows that functional, molecular nanostructures on surfaces fabricated by folding could be just as versatile and specific.

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

Molecular Imaging of Biopolymers Enabled by Electrospray-Ion Beam Deposition

Sabine Abb

Biomolecular functional complexes often serve as inspiration for the development of artificial molecular nanostructures. The functionality of the biomolecular structures is based on complex and adaptable binding motifs that have evolved over billions of years. The detailed understanding of the underlying interactions is pivotal for the rational design and development of new materials, but often difficult to achieve as it requires submolecular resolution. In this thesis, I show how the molecular imaging of biopolymers by scanning tunneling microscopy (STM) and low-energy electron holography (LEEH) contributes to deciphering the structures and the respective binding motifs. These high-resolution imaging methods only perform well on surfaces in ultra-high vacuum (UHV) and for chemically identified species. Thus, electrospray ion beam deposition (ES-IBD) is essential for the controlled deposition for non-volatile species in UHV. The first part of the thesis focuses on the characterization of the disaccharides as smallest representatives of polysaccharides. Deposited by ES-IBD, the first high-resolution STM characterization of this molecular class on a surface in UHV is performed. The disaccharides sucrose and trehalose can be distinguished as they exhibit specific self-assembly motifs and are imaged differently. For sucrose, the two monosaccharide building blocks are resolved, highlighting the impact that high-resolution imaging by STM might have in the future for the clarification of unknown sequences by identifying branching points. In the second part of the thesis, peptides are employed as building blocks for novel structures on the surface. A combined approach of STM imaging with modeling by MD and DFT is applied to identify the binding motifs and the underlying specific interactions. Understanding of the binding motifs of the decapeptide angiotensin-I on Au(111) enables the design of a long-ranged ordered honeycomb network by manipulating the sequence to the octapeptide angiotensin-II. Representing a further binding motif that is often employed in catalytically active peptides, peptide-metal complexes are investigated on the surface showing a significant influence on the peptide structure. Based on the long-range ordered network for the pure angiotensin-II, we find that the introduction of a metal coordination center makes the molecular structure more compact and thus reduces the intermolecular interaction sites yielding an assembly of reduced dimensionality. In the last part, the proof of principle is presented that LEEH, empowered by the ES-IBD sample preparation, is able to image single folded proteins on free stranding ultra-clean graphene and might therefore provide protein structures without averaging. To this end, native mass spectrometry is adopted to ES-IBD for the deposition of folded proteins (cytochrome C, bovine serum albumin) and protein complexes (hemoglobin). In conclusion, the versatile deposition of biopolymers by ES-IBD enables UHV based single molecule imaging techniques for a range of different samples, starting from imaging the sequence and characterizing 2D nanostructures of biomolecules by STM to 3D folded protein complexes imaged by LEEH. High-resolution imaging opens new perspectives for structure determination, such as the branching points of polysaccharides and the 3D structure of single proteins. Moreover, a detailed understanding of binding motifs is crucial for the rational design of new nanostructures.

EPFL2017

Polymorphism in carbohydrate self-assembly at surfaces: STM imaging and theoretical modelling of trehalose on Cu(100)

Sabine Abb, Klaus Kern, Stephan Rauschenbach

Saccharides, also commonly known as carbohydrates, are ubiquitous biomolecules, but little is known about their interaction with surfaces. Soft-landing electrospray ion beam deposition in conjunction with high-resolution imaging by scanning tunneling microscopy now provides access to the molecular details of the surface assembly of this important class of bio-molecules. Among carbohydrates, the disaccharide trehalose is outstanding as it enables strong anhydrobiotic effects in biosystems. This ability is closely related to the observed polymorphism. In this work, we explore the self-assembly of trehalose on the Cu(100) surface. Molecular imaging reveals the details of the assembly properties in this reduced symmetry environment. Already at room temperature, we observe a variety of self-assembled motifs, in contrast to other disaccharides like e.g. sucrose. Using a multistage modeling approach, we rationalize the conformation of trehalose on the copper surface as well as the intermolecular interactions and the self-assembly behavior.