Persistent homology to quantify the quality of surface- supported covalent networks

International audienceCovalent networks formed by on-surface synthesis usually suffer from the presence of a large number of defects. We report on a methodology to characterize such two-dimensional networks from their experimental images obtained by scanning probe microscopy. The computation is based on a persistent homology approach and provides a quantitative score indicative of the network homogeneity. We compare our scoring method with results previously obtained using minimal spanning tree analyses and we apply it to some molecular systems appearing in the existing literature

Investigation of low-dimensional supramolecular architectures by low-temperature scanning tunneling microscopy

In this thesis we report investigations on supramolecular architectures assembled at well-defined metal surfaces. Supramolecular chemistry is dedicated to the study and use of non-covalent interactions to build highly organized molecular arrangements, aiming ultimately at creating systems with tailored properties and useful functions. The adaptation of its powerful principles to fabricate molecular systems at surfaces has already been proven to be very promising; the extended possibilities for the choice of on the one hand molecules with defined size, shape, symmetry and function, and on the other hand substrates with controlled composition, symmetry and patterning allow for a quasi-infinite tuning of the structure and properties of the respective assemblies. The Scanning Tunneling Microscope (STM) is a tool particularly efficient for the nanoscale elucidation of supramolecular systems at surfaces, simultaneously providing topographic and spectroscopic information at the single-atom level. In this regard, a new Low-Temperature STM (LT-STM) operational at temperatures in the range 5 to 400 K has been constructed. A detailed description of the instrument is provided and the demonstration of its exquisite performance represents a major achievement. In addition to local STM studies, complementary experiments were performed with a synchrotron radiation source using integral techniques, namely X-ray Absorption Spectroscopy (XAS) and X-ray Magnetic Circular Dichroism (XMCD). We present results obtained with the linear organic linker 1,4-benzenedicarboxylic acid (terephthalic acid - TPA) on the Au(111), Cu(111) and Cu(100) surfaces. The three-dimensional design principles of supramolecular chemistry could be successfully adapted to these low-dimensional systems. TPA molecules adsorbed on Au(111) organize in two-dimensional molecular sheets, wherein the typical one-dimensional hydrogen-bonded chain motif is found. We show that the inhomogeneities induced by the surface reconstruction can be used to examine the response of the supramolecular self-assembly. In particular, variations in the hydrogen bond length of up to 20% are encountered. On Cu(111), a strict commensurability of the supramolecular sheet to the substrate is not possible because of the reduced lattice spacing of the latter, and the creation of defects is analyzed. Due to their peculiar reactivity, the elbow sites of the reconstructed Au(111) surface act as nucleation centers in the epitaxial growth of transition metals (Fe, Co, Ni), leading to the formation of regular arrays of nanoscale metallic islands. We take advantage of this patterning to steer the formation of metallosupramolecular nano-architectures. Co-deposited TPA molecules attack both Fe and Co clusters and metal-carboxylate linkages evolve. Depending on the deposition parameters, nanoporous grids, mesoscopically organized stripes or truly one-dimensional linkages are obtained. Furthermore, the dynamics of the formation of the nanogrids are monitored in situ. Finally, we report investigations of the magnetic and electronic properties of surface-supported coordination architectures by means of XAS and XMCD. We studied Fe-terephthalate systems engineered on a Cu(100) substrate. Both mononuclear Fe(TPA)4 compounds and diiron centers structures in 2D Fe-TPA lattices exhibit a paramagnetic behavior. Moreover, we demonstrate the decisive influence of the ligand rather than the substrate on the electronic ground state of the metal centers, thus illustrating new vistas to effectively tailor the valence state and magnetic moment of transition metal atoms at surfaces

A Surface Enhanced Raman Spectroscopy study of aminothiophenol and aminothiophenol-C60 self-assembled monolayers: evolution of Raman modes with experimental parameters

International audienceP-aminothiophenol (PATP) is a well known molecule for the preparation of self-assembled monolayers on gold via its thiol functional group. After adsorption, it has been demonstrated that this molecule is anchored to gold through its thiol group, and standing nearly upright at the surface with the amino functional group on top. This molecule has been extensively studied by Surface Enhanced Raman Spectroscopy but its exact SERS spectrum remains unclear. Here we demonstrate that it can be strongly affected by at least two experimental parameters: laser power and layer density. Those features are discussed in terms of a dimerization of the PATP molecules. The free amino group affords the adsorption of other molecules, like C60. In this case, a complex multilayer system is formed and the question of its precise characterisation remains a key point. In this article, we demonstrate that surface enhanced Raman spectroscopy combined with X-Ray photoelectron spectroscopy can bring very important information about the organisation of such a self-assembled multilayer on gold. In our study, the strong evolution of Raman modes after C60 adsorption suggests a change in the organisation of aminothiophenol molecules during C60 adsorption. These changes, also observed when the aminothiophenol layer is annealed in toluene, do not prevent the adsorption of C60 molecules

Electronic structure of single-walled carbon nanotubes on ultrathin insulating films

The electronic structures of single-walled carbon nanotubes on Ag(100) and on ultrathin insulating NaCl(100)/Ag(100) were studied using low-temperature scanning tunneling microscopy. The Fermi level of the nanotubes was shifted toward the conduction band on Ag(100), while it was shifted toward the valence band on NaCl films. We explain this opposite behavior by different basic mechanisms accounting for the Fermi level shifts. On the metal surface, the work function difference between the tube and the substrate determines the direction of the Fermi level shift. In the case of carbon nanotubes on insulating films, the electric field resulting from the dipole moment formed at the interface between the insulating film and the metal plays a decisive role in determining the Fermi level.open8

Grafting a homogeneous transition metal catalyst onto a silicon AFM probe: a promising strategy for chemically constructive nanolithography

International audienceWe report a novel approach to chemically selective lithography using an atomic force microscope (AFM) probe with immobilized homogeneous catalyst, potentially giving access to diverse nanoscale transformations of the surface-bound functional groups. This new concept was proven for the local epoxidation of an alkene-terminated self-assembled monolayer on silicon using H2O2 as an oxidant and a catalytic silicon AFM tip charged with manganese complexes with 1,3,7-triazacyclononane type ligands

Bottom-up synthesis of porphyrin based graphene nanoribbons and nanomeshes

International audienceThe outstanding properties of graphene strongly inspire the scientific community at both the fundamental and applicative levels for high performance electronics, low power spintronics, renewable energy, composites materials and biomedicine. However, along this way several key scientific issues have to be addressed and one of the main challenges is the control and modification of graphene electronic properties, and notably the controlled opening of a sizable bandgap. This can be achieved by quantum confinement, by means of the fabrication of nano-objects with a precise control of the topology, edge-effects... As a consequence, two main graphene forms have emerged for electronic applications, Graphene NanoRibbons (GNR) and Graphene NanoMeshes (GNM). For the last decade, a great attention has been paid to the fabrication of GNRs and GNMs using conventional top-down approach (lithography, etching, thermal treatments). However, this approach does not allow manipulating the material at the atomic scale. In order to truly control the morphology and the composition of the materials and of its edges, the bottom-up approach is the relevant way to proceed. Recently, graphene incorporating porphyrin molecules have been designed either by the groups of Barth and Fischer. Here we report on the synthesis of porphyrin derivatives that can lead to nitrogen doped GNR and GNM. The strategy we applied was to design building blocks based on porphyrins with halogens connectors and polymerize them on metallic surface under Scanning Tunnelling Microscope (STM). We succeeded in the synthesis of two original porphyrins with reasonable yield. The first one is a tetrabromoanthracenyl porphyrin (BrTAP, Fig. 1) with four connectors for the formation of a 2D nanostructure and a second, a bis-bromoanthracenylporphyrin (BrBAP) with two connectors GNR. Preliminary STM image for BrTAP on Ag (111) is shown Fig. 1 and other catalytic surfaces are under investigation to form GNR and GNM

Electronic modulations in a single wall carbon nanotube induced by the Au(111) surface reconstruction

The structural and electronic structure of single wall carbon nanotubes adsorbed on Au(111) has been investigated by low-temperature scanning tunneling microscopy and spectroscopy. The nanotubes were dry deposited in situ in ultrahigh vacuum onto a perfectly clean substrate. In some cases, the native herringbone reconstruction of the Au(111) surface interacted directly with adsorbed nanotubes and produced long-range periodic oscillations in their local density of states, corresponding to charge transfer modulations along the tube axis. This effect, however, was observed not systematically for all tubes and only for semiconducting tubes. © 2015 AIP Publishing LLCclose0

Electronic structure of tetra(4-aminophenyl)porphyrin studied by photoemission, UV–Vis spectroscopy and density functional theory

The valence and conduction bands of a thin film of tetra(4-aminophenyl)porphyrin (TAPP) are investi-gated by direct and inverse photoemission as well as by comparison to density functional theory (DFT)calculations. By projecting the electronic eigenfunctions onto the molecular framework it was possibleto interpret the origin of each spectroscopic feature. Although the majority of the photoemission spec-trum is attributed to the unsubstituted tetraphenylporphyrin (TPP) parent molecule, several featuresare clearly due to the amino substitution. Substitution also has important consequences for the energypositions of the frontier orbitals and therefore on the low-energy electronic excitations. The measuredelectronic transport energy gap (Eg= 1.85 eV) between the highest occupied molecular orbital (HOMO)and lowest unoccupied (LUMO) in TAPP is found to be significantly reduced with respect to TPP. More-over, an increased energy separation between the two highest occupied states (HOMO and HOMO−1) isfound both experimentally and by DFT calculations. Such evidence is attributed to an increased HOMOorbital destabilization due to an enhanced electron-donor character of the phenyl substituents uponamino functionalization. Finally, the above findings together with further time-dependent DFT calcula-tions are used to interpret the effect of the amino groups on the UV–Vis absorption spectrum, namely anoverall red-shift of the spectrum and remarkable intensity changes within the Q band.© 2017 Elsevier B.V

Structures of DPAGT1 explain glycosylation disease mechanisms and advance TB antibiotic design

Summary: Protein N-glycosylation is a widespread post-translational modification. The first committed step in this process is catalysed by dolichyl-phosphate N-acetylglucosamine-phosphotransferase DPAGT1 (GPT/E.C. 2.7.8.15). Missense DPAGT1 variants cause congenital myasthenic syndrome and disorders of glycosylation. In addition, naturally-occurring bactericidal nucleoside analogues such as tunicamycin are toxic to eukaryotes due to DPAGT1 inhibition, preventing their clinical use. Our structures of DPAGT1 with the substrate UDP-GlcNAc and tunicamycin reveal substrate binding modes, suggest a mechanism of catalysis, provide an understanding of how mutations modulate activity (thus causing disease) and allow design of non-toxic “lipid-altered” tunicamycins. The structure-tuned activity of these analogues against several bacterial targets allowed the design of potent antibiotics for Mycobacterium tuberculosis, enabling treatment in vitro, in cellulo and in vivo, providing a promising new class of antimicrobial drug