Nanopatterning of a Covalent Organic Framework Host-Guest System

We have used a boroxine-based COF as a template for C60-fullerene self-assembly on graphite. Local removal of the COF by STM based nanomanipulation creates nanocorrals that may host other species

Supramolecular design of hydrogen-bonded architectures via surface self-assembly of carboxylic building blocks

Crystal engineering deals with the design of ordered arrays of molecular building blocks and is of high importance in nanotechnology, electronics and in the pharmaceutical industry. While organic synthesis provides access to a wide range of molecules, control over their intermolecular interactions is the major challenge taken on by crystal engineering. This thesis focuses on the surface self-assembly of carboxylic acids, as a convenient model system to study general factors governing self-assembly. It is a step towards the rational design of materials with desired compositions, morphologies and functionalities.Specifically, this thesis presents a systematic investigation of hydrogen-bonded (H-bonded) assemblies of carboxylic building blocks on surfaces (i.e. 2D crystals), complemented by studies of their assemblies in bulk solid state (i.e. 3D crystals). This work provides new insights into the complex relationship between building block structures, H-bonding synthons and self-assembly outcomes using scanning tunneling microscopy (STM), X-ray diffraction crystallography and quantum-mechanical calculations. Consideration of these insights has resulted in the supramolecular design of novel self-assembled molecular networks (SAMNs), described below.To elucidate the effect of building block structure on self-assembly, architectures formed by cyclic homo-dimers of carboxylic groups (i.e. structures containing the R22(8) synthon) are analyzed. Results are given in the form of case-studies covering formation of H-bonded macrocycles, chains, ladders, rotaxanes, catenanes and various 2D and 3D nets. Similar analyses of other H-bonding carboxylic acid assemblies are used to highlight the most important aspects of the carboxylic group's supramolecular reactivity, as well as the applications thereof.A detailed study of the surface co-assembly of trimesic acid (TMA) with n-alcohols is presented. Investigating this single system allows for the observation of a wide variety of phenomena that were previously only studied separately, and on structurally different systems. This enables relevant comparisons between molecular structure and the many factors governing self-assembly at the liquid-solid interface. The periodicity and fine structure of the TMA-alcohol SAMN is conveniently modulated by varying n-alcohol length and parity, representing an important step towards rational molecular nanopatterning of surfaces using the principles of crystal engineering.Relationships between building block structures and the stability of resulting carboxylic homosynthons (viz. the cyclic dimer R22(8), the trimer R33(12) and the hexamer R66(24)) are established through a combination of empirical observations and quantum-chemical calculations. Thus, formation of specific homosynthons is found to depend strongly upon steric intermolecular interactions, as well as upon the relative packing efficiencies of competing polymorphs. These findings allow explanation of the structure and chiral nature of the self-assembly formed by terthienobenzenetricarboxylic acid (TTBTA). Additionally, the rational design of supramolecular networks formed by the R66(24) homosynthon is demonstrated for the first time, using triethynylbenzenetricarboxylic acid (TEBTA).Finally, porous TMA networks are used as host matrices to control and study the self-assembly of new π-functional guest molecules. Specifically, two semiconducting heterocirculenes (sulflower and selenosulflower) are imaged by STM with sub-molecular resolution, enabling the study of adsorption-desorption dynamics, host-guest interactions, and stable π-π stacking architectures. The latter findings open up the possibility to form multilayers of host-guest architectures with high potential for applications in optoelectronic devices.L'ingénierie des cristaux de solides moléculaires est un domaine en plein essor, combinant de nombreux aspects de la chimie des matériaux. Il est d'une grande importance pour l'électronique, la nanotechnologie ainsi que pour l'industrie pharmaceutique, ou il y a grand besoin de concevoir des réseaux ordonnés de molécules. Alors que la synthèse organique donne accès à un grand éventail de molécules, le contrôle des interactions intermoléculaires entre celles-ci est le défi pris en charge par l'ingénierie des cristaux. Cette thèse se concentre sur l'auto-assemblage d'acides carboxyliques en surface, en utilisant ce dernier comme modèle pour étudier les facteurs généraux gouvernant l'auto-assemblage. Cette étude constitue une étape vers la conception rationnelle de matériaux ayant des compositions, morphologies et fonctionnalités tels que souhaitées.Plus précisément, cette thèse présente une étude systématique de l'assemblage de certains blocs carboxyliques en surface (i.e. des cristaux 2D), complétée par des études de leurs assemblées à l'état solide (i.e. des cristaux 3D). Ce travail apporte un nouvel éclairage sur la relation complexe entre la structures des blocs, des synthons liées par des ponts hydrogènes et l'auto-assemblage final. Cette étude met en oeuvre la microscopie à effet tunnel (STM), la cristallographie par diffraction des rayons-X et des calculs a base de mécanique quantique. La nouvelle compréhension établie par cette étude a permis d'aboutir à la conception de nouveaux réseaux moléculaires auto-assemblees (SAMNs), décrit ci-dessous.Pour élucider l'effet de la structure des blocs sur l'auto-assemblage, les architectures formées par des homo-dimères de groupes carboxyliques (c'est-a-dire par des structures contenant le synthon R22(8)) sont analysées. Les résultats sont donnés sous la forme d'études de cas, portant sur la formation de macrocycles (liées par des ponts hydrogènes), de chaînes, d'échelles, de rotaxanes, de caténanes et de divers filets en 2D et en 3D. Des analyses similaires d'autres ensembles d'acides carboxyliques sont utilisés pour mettre en évidence les aspects les plus importants de la réactivité supramoléculaire du groupe carboxylique, ainsi que de l'utilité de celle-ci.Une étude détaillée du co-assemblage de l'acide trimésique (TMA) avec des n-alcools est présenté. La recherche complétée sur ce système permet l'observation d'un grand éventail de phénomènes n'ayant été qu'étudiés séparément. Entre autre, cela permet des comparaisons pertinentes entre structure moléculaire et les nombreux facteurs qui régissent l'auto-assemblage à l'interface liquide-solide. La structure fine et la périodicité du SAMN TMA-alcool est modulée simplement, en faisant varier la longueur et la parité des n-alcools. Ceci représente une étape importante vers la nanostructurisation rationnelle des surfaces avec des molécules, en utilisant les principes de l'ingénierie des cristaux.Les relations entre les structures des blocs et la stabilité des homosynthons carboxyliques qui en resultent (à savoir le dimère cyclique R22(8), le trimère R33(12) et l'hexamère R66(24)) sont établies par une combinaison d'observations empiriques et de calculs émanant de la chimie quantique. Ainsi, la formation d'homosynthons spécifiques se trouve à dépendre fortement des interactions stériques intermoléculaires, ainsi que de l'efficacité relative des polymorphes qui résultent de l'assemblage. Ces résultats permettent l'explication de la structure et de la nature chirale de l'auto-assemblage formé par l'acide terthienobenzenetricarboxylic (TTBTA). En outre, la conception rationnelle des réseaux supramoléculaires formés par l'homosynthon R66(24) est démontré pour la première fois, a l'aide de l'acide triethynylbenzenetricarboxylic (TEBTA).Enfin, les réseaux poreux TMA sont utilisées comme matrices d'accueil pour contrôler et étudier l'auto-assemblage de nouvelles molécules π-fonctionnelles

Reactivity on and of Graphene Layers: Scanning Probe Microscopy Reveals

Chapters "Mechanistic insights into surface-supported chemical reactions", "Reactivity on and of Graphene Layers: Scanning Probe Microscopy Reviels" and "Bottom-up fabrication of atomically precise graphene nanoribbons" of this book are ...status: Published onlin

Stabilization of exotic minority phases in a multicomponent self-assembled molecular network

Trimesic acid (TMA) and alcohols were recently shown to self-assemble into a stable, two-component linear pattern at the solution/highly oriented pyrolytic graphite (HOPG) interface. Away from equilibrium, the TMA/alcohol self-assembled molecular network (SAMN) can coexist with pure-TMA networks. Here, we report on some novel characteristics of these non-equilibrium TMA structures, investigated by scanning tunneling microscopy (STM). We observe that both the chicken-wire and flower-structure TMA phases can host 'guest' C60 molecules within their pores, whereas the TMA/alcohol SAMN does not offer any stable adsorption sites for the C60 molecules. The presence of the C60 molecules at the solution/solid interface was found to improve the STM image quality. We have taken advantage of the high-quality imaging conditions to observe unusual TMA bonding geometries at domain boundaries in the TMA/alcohol SAMN. Boundaries between aligned TMA/alcohol domains can give rise to doubled TMA dimer rows in two different configurations, as well as a tripled-TMA row. The boundaries created between non-aligned domains can create geometries that stabilize TMA bonding configurations not observed on surfaces without TMA/alcohol SAMNs, including small regions of the previously predicted 'super flower' TMA bonding geometry and a tertiary structure related to the known TMA phases. These structures are identified as part of a homologic class of TMA bonding motifs, and we explore some of the reasons for the stabilization of these phases in our multicomponent system

Structural Insights into the Mechanism of Chiral Recognition and Chirality Transfer in Host-Guest Assemblies at the Liquid-Solid Interface

© 2018 American Chemical Society. Understanding structure-efficiency relationships in chiral recognition and chirality transfer constitutes an important step toward the rational design of improved chiral probes and chirality auxiliaries or inducers. Recently discovered enantioselective host-guest adsorption opened a new pathway toward the enantioselective reconstruction of on-surface monolayers. In this study, we explored the importance of size matching between host cavity and chiral guest for the efficiency of chiral recognition and subsequent chirality induction in the initially racemic host.status: publishe

Manifestations of Non-Planar Adsorption Geometries of Lead Pyrenocyanine at the Liquid-Solid Interface

In this work, we provide evidence for multiple non-planar adsorption geometries of a novel pyrenocyanine derivative at the liquid-solid interface under ambient conditions. When adsorbed at the organic liquid-solid interface, lead pyrenocyanine forms well-ordered monolayers that exhibit peculiar non-periodic contrast variation. The different contrast of the adsorbed molecules is attributed to dissimilar adsorption geometries which arise from the non-planar conformation of the molecules. The non-planarity of the molecular backbone in turn arises due to a combination of the angularly extended pyrene subunits and the presence of the large lead ion, which is too big to fit inside the central cavity and thus is located out of the aromatic plane. The two possible locations of the lead atom, namely below and above the aromatic plane, could be identified as depression and protrusion in the central cavity, respectively. The manifestation of such multiple adsorption geometries on the structure of the resultant monolayer is discussed in detail. The packing density of these 2D arrays of molecules could be tuned by heating of the sample wherein the molecular packing changes from a low-density, pseudo six-fold symmetric to a high-density, two-fold symmetric arrangement. Finally, a well-ordered two-component system could be constructed by incorporating C60 molecules in the adlayer of lead pyrenocyanine at the liquid-solid interface.status: publishe

Insights into dynamic covalent chemistry at surfaces

The potential of surface confined self-assembly to influence the chemical equilibrium of Schiff base formation and bias the yield and distribution of reaction products is exploredcrosscheck: This document is CrossCheck deposited related_data: Supplementary Information copyright_licence: The Royal Society of Chemistry has an exclusive publication licence for this journal copyright_licence: The accepted version of this article will be made freely available in the Chemical Sciences Article Repository after a 12 month embargo period history: Received 19 August 2015; Accepted 11 September 2015; Advance Article published 25 September 2015; Version of Record published 3 November 2015status: publishe

Supramolecular ordering in oligothiophene−fullerene monolayers

Scanning tunneling microscopy (STM) of monolayers comprising oligothiophene and fullerene molecular semiconductors reveals details of their molecular-scale phase separation and ordering with potential implications for the design of organic electronic devices, in particular future bulk heterojunction solar cells. Prochiral terthienobenzenetricarboxylic acid (TTBTA) self-assembles at the solution/graphite interface into either a porous chicken wire network linked by dimeric hydrogen bonding associations of COOH groups (R22(8)) or a close-packed network linked in a novel hexameric hydrogen bonding motif (R66(24)). Analysis of high-resolution STM images shows that the chicken wire phase is racemically mixed, whereas the close-packed phase is enantiomerically pure. The cavities of the chicken wire structure can efficiently host C60 molecules, which form ordered domains with either one, two, or three fullerenes per cavity. The observed monodisperse filling and long-range co-alignment of fullerenes is described in terms of a combination of an electrostatic effect and the commensurability between the graphite and molecular network, which leads to differentiation of otherwise identical adsorption sites in the pores

The impact of grafted surface defects and their controlled removal on supramolecular selfassembly

We demonstrate the use of covalently modified graphite as a convenient and powerful test-bed for the versatile investigation and control of 2-D crystallization at the liquid solid interface. Grafted aryls act as surface defects and create barriers to supramolecular self-assembly. An easily tunable grafting density allows for varying the effect of such defects on supramolecular self-assembly. Finally, the defects can be locally removed, triggering monolayer reconstructions and allowing in situ investigations of thermodynamically unstable or metastable morphologies.We demonstrate the use of covalently modified graphite as a convenient and powerful test-bed for the versatile investigation and control of 2-D crystallization at the liquid solid interface. Grafted aryls act as surface defects and create barriers to supramolecular self-assembly. An easily tunable grafting density allows for varying the effect of such defects on supramolecular self-assembly. Finally, the defects can be locally removed, triggering monolayer reconstructions and allowing in situ investigations of thermodynamically unstable or metastable morphologies.status: publishe