Dissertations / Theses on the topic 'Supramolecular Self-assembly - Molecules'

Das grundlegende Verständnis der Adsorption, der Eigenschaften, und der Wechselwirkungen von komplexen organischen Molekülen auf Festkörperoberflächen ist für die Entwicklung neuer Anwendungen in der Nanotechnologie von entscheidender Bedeutung. Die in dieser Arbeit untersuchten funktionellen Bausteine gehören zu den Porphyrinen und Phthalocyaninen. Deren Adsorption, elektronische Struktur, und Reaktionen der Moleküle auf Edelmetalloberflächen wurden mit mehreren Methoden charakterisiert, insbesondere der Rastertunnelmikroskopie, Rastertunnelspektroskopie, Röntgen-Nahkanten-Absorptions-Spektroskopie und Photoelektronenspektroskopie, welche zudem durch theoretische Simulationen unter Verwendung der Dichtefunktionaltheorie ergänzt wurden. Tetra(p-hydroxyphenyl)porphyrin Moleküle ordnen sich durch Selbstorganisation zu verschiedenen, durch Wasserstoffbrückenbindungen stabilisierten Nanostrukturen an, welche in Abhängigkeit von dem Substratoberflächengitter untersucht wurden um das komplizierte Zusammenspiel von Molekül−Molekül und Molekül−Substrat-Wechselwirkungen bei der Selbstorganisation zu verstehen. Erhitzen der Adsorbatschichten dieses Moleküls führt zu einer schrittweisen Deprotonierung, und außerdem konnte auch ein Schalten der Leitfähigkeit einzelner Porphyrin-Moleküle durch lokale Deprotonierung mittels Spannungspulsen demonstriert werden. Eine Polymerisationsreaktion, welche auf der Ullmann-Reaktion basiert, aber direkt auf einer Oberfläche stattfindet, wurde für Kupfer-octabromotetraphenylporphyrin Moleküle, die auf Au(111) adsorbiert sind, gefunden. Nach einer thermischen Abspaltung der Bromatome von den Molekülen reagieren dabei die Radikalmoleküle bei hohen Temperaturen miteinander und bilden geordnete, kovalent gebundene Netzwerke aus. Die Bromabspaltung und die nachfolgenden Reaktionen und Veränderungen der elektronischen Struktur der Moleküle wurden ausführlich für die Substratoberflächen Au(111) sowie Ag(110) untersucht. Weiterhin, wird die Adsorption und Selbstorganisation von metall-freien Phthalocyanin-Molekülen auf einer Ag(110)-Oberfläche, und deren Selbstmetallierungsreaktion mit Silberatomen des Substrats umfassend und verständlich beschrieben. Zuletzt wurden organische Hybrid-Grenzflächen zwischen verschiedenen Metall-Phthalocyaninen untersucht, wobei ein Ladungstransfer zwischen Kobalt- und Platin-Phthalocyanin-Molekülen gefunden wurde. Dotierung gemischter Metall-Phthalocyanin-Filme durch Einlagerung von Kaliumatomen und deren selektive Adsorption im Molekülgitter führt zu einer deutlichen Veränderung der elektronischen Eigenschaften, aufgrund einer Ladungsübertragung an die Kobalt-Phthalocyanin Moleküle.

Loline alkaloids (LA) are secondary metabolites produced by Epichloandamp;euml; (anamorph, Neotyphodium) grass endophytes. They are toxic and deterrent to a broad range of herbivorous insects but not to livestock. This protective bioactivity has spurred considerable research into the LA biosynthetic pathway. LOL, the gene cluster containing nine genes, is required for LA biosynthesis. The regulation of LOL genes during LA production in culture and in symbio is of interest. In this study, coordinate regulation between LOL gene expression and LA production level was investigated in both MM culture and symbiota. Results showed that expression of LOL genes in N. uncinatum MM culture were tightly correlated with each other (p andamp;lt; 0.0005), and all presented a significant temporal quadratic pattern during LA production. Gene expression started before LA were detectable, and increased while LA accumulated. The highest gene expression level was reached before the highest amounts of LA were detected, and gene expression level declined to a very low level after amounts of LA plateaued. Observations suggested that the hierarchical clusters based on the correlation coefficient could help to predict the roles of LOL genes in the LA pathway. In symbiota, coordinate coregulation of LOL gene expression with LA was found in E. festucae-meadow fescue inflorescences and stromata, whereby lower LOL gene expression corresponded with the lower LA level in stromata. In N. uncinatum (or N. siegelii)-meadow fescue vegetative tissues, dramatically higher LA levels were found in younger leaf tissue than in older leaf tissue, yet no evidence was found to relate this difference to LOL gene expression differences. Instead, substrate availability may regulate the LA level. In particular, asparagine was more than 10-fold higher in young leaf tissue than in old tissue, although proline was significantly lower in young tissue. Therefore, different regulatory mechanisms underlie LOL gene expression and LA production in different circumstances. The GUS activity of Pro-lolC2-GUS and Pro-lolA2-GUS in Neotyphodium species was almost undetectable in culture, though the activity could be detected in symbiota. The mRNA of GUS did not exhibit the same pattern as lolC2 or lolA2 in culture during LA production time course. A Pro-lolC2-cre transgene was expressed in complex medium, in which lolC2 mRNA was not detectable. These results suggest that proper regulation of LOL genes in culture or symbiota is dependent on the LOL cluster.

Cette thèse se focalise sur la synthèse et l'étude de nouvelles molécules photoactives et leurs applications en tant que marqueurs, senseurs moléculaires et récepteurs d’ions photomodulables en milieux aqueux et organisés. Les fluorophores développés sont principalement des dérivés du bore-dipyrométhene (BODIPY), comportant des groupements réactifs (azoture, perfluorophényle), des chaines hydrophobes, ou sont intégrés à un récepteur de calcium biocompatible. Le développement d'architectures auto-assemblées multicompartimentées de type vésicules dans des polymersomes géant y est décrit. Ces architectures ont été utilisées pour la génération de lumière blanche dans un micro-domaine, et constitue un modèle pour l'étude de transfert d'ions calcium entre vésicules localisées dans des polymersomes individuels. Ce transfert entre nano-objets confinés à l'intérieur d'un polymersome géant représente un système prototype de communication cellulaire artificiel rudimentaire
The thesis focuses on the study and design of novel photoactive molecules and their application as labeling agents, fluorescent molecular Ca2+-sensors and photolabile Ca2+-decaging agents in aqueous media and organized supramolecular assemblies. The designed fluorophores are based on boron-dipyrromethene (BODIPY) bearing hydrophobic chains or a reactive group like an azide or a perfluorophenyl moiety. Biocompatible calcium receptors have been prepared harnessing the fluorescence properties of BODIPY, naphthalimide and furan fluorophores. The development of self-assembled multicompartmentalized architectures, namely fluorocarbon vesicles in giant polymersomes is reported and the system has been used to create white light emission in confined microdomains. The Ca2+-based ion transfer ion the confined polymer compartments between individual fluorinated vesicles has been studied. The ion transfer in between vesicles in polymer microcompartments has been established as an artificial prototype system for cellular communication

Ce mémoire décrit la synthèse d’hôtes organiques et organométalliques contenant des motifs riches en électrons, particulièrement le tétrathiafulvalène (TTF), pour la complexation supramoléculaire de fullerènes C60 et C70. Le chapitre 1 est une revue de la littérature qui présente les notions de cavitant, de métallocavitant et des hôtes supramoléculaires. Le chapitre 2 présente les méthodes de caractérisation utilisées dans ce travail. Le chapitre 3 est consacré à une nouvelle méthode de synthèse de pinces moléculaires et des récepteurs tripodaux contenant l’unité riche en électrons (TTF). Les pinces triazoles ont été préparées par chimie « clic » entre l'azoture -TTF et des dérivés benzéniques disubstitués en position 1 et 3 par un acétylène. La réaction de l'azoture-TTF et des 1,3, 5-benzènes trisubstitués a donné des récepteurs tripodaux. L'affinité des hôtes avec les fullerènes C60 et C70 a été étudiée par la méthode optique spectroscopique UV-vis dans quatre solvants différents. La constante d’association la plus élevée a été calculée pour l’hôte 4 dans le chlorobenzène. Cependant, le récepteur tripodal n'a pas montré une affinité importante envers les fullerènes. Le chapitre 4 est consacré à la synthèse des nouveaux metallocavitands de zirconium TTF- Zr3 préparés par la méthode d’agrégation. Un seul hôte a été isolé et caractérisé par la méthode spectroscopique. Dans ce chapitre, nous présentons l'étude des interactions supramoléculaires avec les fullerènes en surveillant la réponse UV-vis à l’addition d’une quantité croissante de fullerènes à la solution contenant l’hôte. Le chapitre 5 décrit la synthèse de nouveaux metallocavitants de Zr3 à partir de la réaction de dichlorure de zirconocène sur l'acide carboxylique. Quatre metallocavitants de Zr3 ont été préparés. Les structures cristallographiques, les propriétés photophysiques et leurs utilisations potentielles en tant que matériaux émissifs bleus ont été présentées. Le chapitre 6 est séparé en trois sections. La première section décrit la synthèse et l’affinité de metallocavitant de tantale (V) avec les fullerènes. La deuxième section illustre la tentative de synthèse d’une librairie de Zr3 en utilisant la réaction de couplage croisée. Enfin, la dernière section présente la synthèse du nouveau metallocavitant de Ta3Carbox obtenu par la méthode d’agrégation à partir de la réaction de Cp*TaMe4 avec de l'acide 4 - iodobenzoïque. La structure est étudiée par rayons X.
This thesis described the synthesis of organic and organometallic hosts containing electron rich units in particularly tetrathiafulvalene (TFF) to bind fullerenes C60 and C70. Chapter two illustrates the different analysis techniques used in this thesis. Chapter three described new method for the synthesis of tweezers-like TTF and tripodal TTF molecules in addition to their binding affinity towards fullerenes C60 and C70. The tweezers-like TTF were prepared by click chemistry from azide-TTF and 1,3 substituted benzene. Similarly, the reaction of azide-TTF and 1,3, 5 substituted benzene yielded the tripodal-TTF receptor. The affinity toward fullerenes C60 and C70 were studied in four different solvents. The highest binding constant was calculated for host 4 in chlorobenzene toward fullerene C70. Moreover, solvent dependant behavior was observed with the studied host. However, the tripodal receptor did not showed significant affintity towards fullerenes. Chapter four described the synthesis of new TTF-Zr3 metallocavitand by coordination method; two hosts were isolated and characterized. In this chapter we present the binding study toward fullerenes by monitoring the UV-vis response to increasing amount of fullerenes added to the solution of the host. Chapter five described the synthesis of new Zr3 metallocavitand in one pot reaction from the reaction of zirconocene dichloride with carboxylic acid in aqueous media. Four Zr3 metallocavitand were prepared and the crystallography was presented in addition to the photophysical properties and their potential uses as blue emissive materials. The last chapter is separated into three sections. The first section described our early work on tantalum (V) metallocavitand in addition to their hosting capability toward fullerenes. The second section illustrate the tentative has been committed to the design and synthesis of Zr3 library using cross-coupling reaction in addition to the synthesis of extended Zr3-cinnamate metallocavitand. Lastly, the last section illustrates the synthesis of new Ta3-Carbox achieved by aggregation method from reaction of Cp*TaMe4 with 4-iodobenzoic acid. The single X-ray structure revealed a new structure with trimetallic core comparable to the core observed for tantalum metallocavitand.

Self-assembling molecules are central to a plethora of processes found in nature, biotechnology and even disease. The importance of the non-covalent interaction of monomers to the formation of fibrillar assemblies is evident in the repeated use of this mechanism throughout nature, from essential cellular processes such as the formation of the cytoskeleton to the production of silk. Further, it has been recognised in the last two decades that a self-assembly mechanism, that is the formation of amyloid, underpins the pathology of protein misfolding diseases; it is therefore essential to dissect these mechanisms. Despite recent technological and model system developments, self-assembling molecules remain challenging to investigate. Using combined structural and biophysical characterisations of penta- and hexa-peptide self-assembling model systems these investigations shed further light on the structure of amyloid-like fibrils. The elucidation of the structures of these fibrillar systems not only has implications for disease but also makes them well placed for consideration for biotechnological applications. In reflecting upon how cross-ß structural architectures can be organised in the fibrillar state, a molecular and supramolecular model of fibrils formed by a fragment of !-synuclein is reported. The fibrils are found to consist of a novel and elaborate cross-ß architecture that leads to a helical supramolecular assembly spanning length scales previously unobserved for such a system. Where self-assembly is a useful route to supramolecular structure formation, the use of low molecular weight gelator (LMWG) peptides to create fibrillar structures with defined material properties is also explored. The complex link between molecular structure, self-assembled architecture, fibril formation, fibril interaction and ultimately bulk material properties is described. It is found that the determinants of self-assembly are distinct from the determinants of gelation and so future LMWG design will have to consider both individually. This work presents methodological advances in the characterisation of self-assembled structures. The investigations presented here have relevance for disease related processes but also to the technological use of these systems as materials. Finally, this work emphasises the beauty of the extravagant, yet elegant connection between molecular interaction and supramolecular selfassembly.

Dissertation (PhD)--Stellenbosch University, 2004
ENGLISH ABSTRACT: Over the past decade peptide bola-amphiphiles have been the subject of much attention because of their role as potential models of functionalised membranes and as new generation surfactants. In the quest for new surfactants a peptidomimetic-based approach was used to design a library of novel 'hybrid' bola-amphiphilic peptide surfactants derived from sapecin B and a model symmetrical oligo-glycine bola-amphiphile. The library was divided into different series, each one purpose-built; first, to investigate hierarchal supramolecular architecture and, second, to investigate potential antimicrobial activity. The bola-amphiphiles were synthesised using Fmoc-polyamide based solid phase peptide synthesis and purified via high performance liquid chromatography. The peptide hybrids were characterised using electro spray mass spectrometry, nuclear magnetic resonance, different modes of electron microscopy, Fourier-transform infrared spectroscopy and, in some cases, further studies were done using circular dichroism and bioactivity tests. The model bola-amphiphile suberamide(GGh was synthesised using peptide fragment condensation based on solid phase peptide synthesis. The synthesis is bi-directional (N~C and C~N) and versatile, making it possible to synthesis new dicarboxylic oligopeptide bola-amphiphiles and other analogous compounds. The product, suberarnide(GG)2, was purified using its inherent ability to self-assemble in an acidic solution. Novel asymmetrical bola-amphiphiles composed of dipeptide head groups linked via an aliphatic (I)-amino acid, serving as a hydrocarbon spacer, were also synthesized. Two small libraries of bola-amphiphiles were established - the first involved variation in to-amino acid length and the other variation in the C-terminal amino acid. The bolaamphiphiles were self-assembled in either 0.1% trif1uoroacetic acid or 0.1% triethylamine. Electron microscopy revealed the formation of a variety of higher order supramolecular architectures based on ~-sheet self-assembly. FT-IR spectrometry indicated that interlayer and intralayer hydrogen bond networks, together with strong selfassociation, promoted by the hydrophobic effect and, in certain instances, electrostatic interactions, are responsible for the variety of supramolecular architectures. Variations in the higher order structures can be attributed to amino acid composition, specifically length of m-amino acid, nature of the C-terminal amino acid and the optimised solvent conditions used for the self-assembly process. A third library of novel 'hybrid' bola-amphiphilic peptide surfactants, in which a cationic tripeptide motif from antimicrobial peptides was combined in a hybrid molecule containing a oi-amino acid residue, was established. These bola-amphiphiles displayed potent antimicrobial activity against both Gram-positive and Gram-negative bacteria; the analogues were as active or more active than the leader peptides yet, remarkably, displayed little or no appreciable haemolytic activity. These organopeptide bolaamphiphiles thus demonstrated selective toxicity towards bacteria. The hydrophobicity imparted by the co-amino acid has contrasting effects on haemolysis and antimicrobial activity of the peptide analogues. The other unique feature of these peptides and their analogues is the fact they self-assembled into complex supramolecular architectures, composed primarily of ~-sheets. Their self-assembly is primarily governed by hydrophobic interactions together with inter and intralayer hydrogen bonding. Electron microscopy clearly revealed higher order structures for both peptides and analogues. The generation of higher order supramolecular architecture is dependent on optimisation of ~- sheet self-assembly whereas antimicrobial activity is dependent on the balance between net positive charge and optimum hydrophobicity of the peptide hybrids. This study has demonstrated that it is possible to design hybrid peptide surfactants capable of producing higher order supramolecular architecture and improving the antimicrobial activity whilst reducing the haemolytic effect. The study and design of these versatile 'purpose-built' bio-inspired surfactants heralds a novel approach, one that shows tremendous potential.
AFRIKAANSE OPSOMMING: Die afgelope dekade het bola-amfifiliese peptiede baie aandag geniet weens hulle rolle as potensiële modelle van gefunksionaliseerde membrane en as 'n nuwe generasie surfaktante. In die soeke na nuwe surfaktante is 'n peptiedornimetiese benadering gevolg om 'n biblioteek van nuwe "hibried" bola-amfifiliese peptiedsurfaktante van sapesien B en 'n simmetriese oligoglisien bola-amfifil af te lei. Die biblioteek is in verskillende reekse onderverdeel. Elke reeks is doelmatig vervaardig om ondersoek in te stel na twee aspekte, nl. die rangorde van die supramolekulêre strukture en die potensiële antirnikrobiese aktiwiteit. Fmoc-poliamied gebaseerde soliedefase-peptied-sin-tese is aangewend vir die sintese van die bola-amfifile en hulle is met behulp van hoë doeltreffendheid vloeistofchromatografie gesuiwer. Die peptiedhibriede is gekarakteriseer met behulp van elekrosproei massaspektrometrie, kern-magnetiese resonansie, verskillende modusse elektronrnikroskopie, Fourier-transform infrarooispektrometrie en, in sommige gevalle is verdere studies met sirkulêre dichroïsme en bioaktiwiteitstoetsing uitgevoer. Die bola-amfifilsuberamiedtflfij--model is met behulp van peptiedfragment-konden-sasie gesintetiseer gegrond op soliedefase-peptiedsintese. Dit sintese vind in twee rigtings plaas (N~C en C~N) en is veelsydig aangesien dit die sintese van sowel nuwe dikar-boksielbola- amfifile as ander analoë verbindings moontlik maak. Die produk, suber-arnied(GG)2, is gesuiwer met behulp van die verbinding se inherente vermoë tot self-montering in suur oplossings. Nuwe assimetriese bola-amfifile, saamgestel uit dipeptiedkopgroepe, gekoppel via 'n alifatiese ro-aminosuur, wat as koolwaterstofspasieerder dien, is ook gesintetiseer. Twee klein bola-amfifilbiblioteke is saamgestel - die een het variasies in die ro-aminosuur se lengte omvat en die ander een variasies in die C-terrninale aminosuur. Selfmontering van die bola-amfifile het plaasgevind in of 0,1 % trifluorasynsuur Of 0,1 % trietielamien. Elektronrnikroskopie het die bestaan van 'n verskeidenheid hoërorde supramolekulêre strukture, gegrond op p-plaatselfmontering, aangetoon. Uit FT-IR-spektrometrie blyk dit dat inter - en intralaag waterstofbinbdingsnetwerke en sterk selfassosiasie, 19. word bevorder deur die hidrofobiese effek en, in sekere gevalle, elektrostatiese interaksies, is verantwoordelik vir die verskeidenheid supramolekulêre strukture. Variasies in die hoërorde strukture kan toegeskryf word aan aminosuursamestelling, in besonder die lengte van die ro-aminosuur, die aard van die C-terminale aminosuur en die geoptimiseerde oplosmiddelkondisies wat gebruik is vir die selfmonteringsproses. 'n Derde biblioteek nuwe "hibried" bola-amfifiliese peptiedsurfaktante, waarin 'n kationiese tripeptiedmotief uit antimikrobiale peptiede gekombineer is met 'n m-aminosuurresidu, is geskep. Sommige van hierdie bola-amfifile het 'n kragtige antimikrobiese aktiwiteit teenoor sowel Gram-positiewe as Gram-negatiewe bakterieë gertoon. Die analoë strukture was aktief, of selfs meer aktief as die voorste peptiede maar het, verbasend genoeg, nie 'n beduidende hemolitiese aktiwiteit vertoon nie. Hierdie organopeptied bola-amfifil het dus 'n selektiewe toksisiteit teenoor bakterieë vertoon. Die hidrofo-bisiteit, as gevolg van die ui-aminosuur, het 'n resiproke effek op hemolise en die antimikrobiese aktiwiteit van die peptiedanaloë. Die ander uitstaande kenmerk van die peptiede en hulle analoë is die vermoë om te selfmonteer en komplekse supramolekulêre strukture, bestaande hoofsaaklik uit ~-plate, te vorm. Hierdie selfmontering word in hoofsaak beheer deur hidrofobiese interaksies asook inter - en intralaagwaterstofbinding. Elektronmikroskopie het duidelik hoërorde strukture getoon by sowel dié peptiede as hulle analoë. Die ontwikkeling van hoërorde supramolekulêre struktuurvorms is afhanklik van die optimalisering van die ~-plaatselfmontering. Daarteenoor is die antimikro-biese aktiwiteit afhanklik van die balans tussen die netto positiewe lading en die opti-male hidrofobisiteit van die peptiedhibriede. Hierdie studie het getoon dat dit moontlik is om hibriedsurfaktante te ontwerp wat hoërorde supramolekulêre strukture te produseer en om die antimikrobiese aktiwiteit te verbeter terwyl die hemolitiese effek verminder word. Die studie en ontwerp van hier-die veeldoelige, "doelmatig-gesintetiseerde" biogeïnspireerde surfakante stel 'n unieke benadering daar, wat oor groot potensiaal beskik.

Supramolecular electronics aims to construct and investigate the optoelectronic properties of tailored supramolecular nanoarchitectures. The aim of this thesis is to get control over the organization of organic molecular systems and correlate their structure with the electrical properties, with particular attention at the nanoscale properties. The exploited strategies require a focused molecular design, the balancing of intermolecular and interfacial interactions, a control on the kinetics of the processes and possibly the exploitation of external forces. The presented results showed that understanding the local properties of a material on a nanoscale basis is a huge fundamental challenge to bring solutions to both scientific and technological issues, since in electronic devices the performances are strongly dependent on the order at the supramolecular level.

Dynamic combinatorial chemistry (DCC) is a powerful method for synthesising complex molecules and identifying unexpected receptors. Chapter 1 gives an overview of the concept of DCC and its applications, and discusses its evolution to date. Chapter 2 describes the discovery of a new generation of donor-acceptor [2]catenanes in aqueous dynamic combinatorial systems. The assembly of these [2]catenanes is promoted by a high salt concentration (1 M NaNO3), which raises the ionic strength and encourages hydrophobic association. More importantly, a mechanism that explains and predicts the structures formed is proposed, giving a fundamental insight into the role played by hydrophobic effect and donor-acceptor interactions in this process. Building on these results, Chapter 3 describes the assembly in high salt aqueous libraries of a larger structure: a [3]catenane. Remarkably, the [3]catenane exhibits strong binding interactions with a biologically relevant target - spermine - in water under near-physiological conditions. Its synthesis is improved if the salt is replaced by a sub-mM concentration of spermine, acting as a template. Chapter 4 explores in further detail how subtle variations in the building block design influence the selective formation of either [2] or [3]catenanes. This last section underlines both the advantages and the limitations of the method developed in Chapter 3. After a short conclusion (Chapter 5), Chapter 6 gives experimental details.

Le travail décrit dans cette thèse couvre une étude fondamentale sur des canaux artificiels d'eau et sur des matériaux membranaires incorporant ces canaux. Structuré en quatre chapitres, la thèse commence par une présentation de l'état de l’art sur les systèmes biomimétiques de transport d'eau et des membranes biomimétiques. Au centre de tous ces travaux de recherche sont les protéines biologiques hautement efficaces et sélectives, les Aquaporines. Le deuxième chapitre présente les canaux artificiels d'eau à base d'imidazole-quartet. Les similitudes structurelles et fonctionnelles avec les Aquaporines sont discutées et caractérisées par plusieurs méthodes expérimentales. Les structures à l'état solide obtenues à partir de monocristaux présentent une organisation très similaire des I-quartets avec leurs homologues biologiques. Le biomimétisme fonctionnel du transport de l'eau a été démontré par des expériences cinétiques de transport à travers des systèmes vésiculaires. Le mécanisme de translocation de l'eau et l'organisation confinée dans des environnements lipidiques a été confirmé par des simulations dynamiques moléculaires, tandis que la preuve physique de l'eau orientée dipolaire dans les canaux intégrés aux lipides a été fournie par des expériences de spectroscopie IR polarisée. Le troisième chapitre présente de nouveaux canaux d'eau artificiels en utilisant une stratégie d'auto-assemblage. De nouveaux composés à base de diol, de tétrazacrown et de tryarilamine capables de transporter l'eau sont décrits. Le dernier chapitre décrits le passage du niveau moléculaire aux matériaux membranaires macroscopiques incorporant des canaux d'eau artificiels. Deux configuration membranaires différentes ont été décrites: des membranes en couche mince par l'incorporation de nanoparticules à base d'imidazole dans des polymères de polyamide et des membranes de la cellulose régénérée chimiquement greffée par des monomères de canaux d'eau artificiels. Les membranes ont été caractérisées par diverses méthodes d'imagerie et d'analyse et leurs performances ont été testées dans des expériences d'osmose inverse et de filtration d'osmose directe. La thèse est conclue avec une partie de conclusion générale, comprenant des perspectives pour les développements futurs
The work described in this thesis covers an in depth fundamental study of artificial water channels and of membrane materials incorporating these channels. Structured in four chapters, the thesis begins with a presentation of the state of the art in the field of biomimetic systems and membranes for water transport. The center of the described research work is the family of highly efficient and selective biological water transporter proteins, the Aquaporins. The second chapter presents the description of imidazole-quartet supramolecular artificial water channels. Structural and functional similarities with Aquaporins are discussed and based on several experimental methods. Single-solid state structures present very similar organization of confined water wires as found in their biological counterparts. Functional mimicry of water transport has been proved through stopped flow experiments in vesicular systems. Further characterization concerning water translocation mechanism and confined organization in lipid environments have been obtained through molecular dynamic simulations, while physical evidence of dipolar oriented water in lipid embedded channels has been provided by sum frequency generation experiments. The third chapter presents novel artificial water channels. New diol, tetrazacrown and tryarilamine based compounds have been described, with a main focus on design, synthesis, self-assembly and water transport properties. The last chapter makes the transition from the molecular systems to macroscopic membrane materials incorporating artificial water channels. Two different approaches have been described: thin film nanocomposite membranes based on the incorporation of imidazole-quartet nanoparticles in polyamide polymers and chemically grafted regenerated cellulose membrane through the use of custom monomers for the obtaining of artificial water channels. The membranes have been characterized through various imaging and analytical methods and their performances have been tested in reverse and forward osmosis experiments. The thesis is concluded with a general conclusion part, including perspectives for future developments

This work describes an investigation into the solution-phase binding of anionic guests by bimacrocyclic lanthanide complexes. It outlines the preparation of different classes of complexes bearing two metallic domains, and the effects of association on both the complex and the guest. Chapter one provides a cursory introduction to the fundamental properties of the lanthanides with a focus on luminescence. A brief literature review is given on the use of emissive lanthanide probes for the sensing of analytes. Chapter two concerns the preparation and properties of a series of binuclear complexes in which the two centres are linked with a short spacer group, with the aim of selectively sequestering small anions such as the halides in solution. The concept of luminescence titration will be introduced and then used to assess the binding parameters of a selection of guests. Chapter three describes a related class of ditopic lanthanide complexes in which the two metal centres are separated by a semi-rigid butyne linking group. Luminescence studies are again used to evaluate the binding constants of homologous series of dianions to ascertain how the size, geometry and functionalization of the anionic guest impacts on binding. Chapter four explores the coordination of phosphate species and assesses the ability to bind biologically significant phosphates of some of the complexes from Chapter 3. Chapter five details an investigation into the effects on guest-selectivity of further lengthening the linking unit which separates the two macrocyclic binding domains. Chapter six summarises the work done throughout the thesis and draws some overarching conclusions, as well as highlighting areas for further study. Chapter seven describes the experimental procedures.

El presente trabajo tiene por objetivo el diseño y la síntesis de diferentes oligómeros de guanidina bicíclica, así como el estudio de sus propiedades. El grupo guanidinio es conocido por su capacidad para interaccionar con aniones (especialmente oxonaniones) mediante puentes de hidrógeno e interacciones de tipo electrostático. Los primeros capítulos de esta tesis están dedicados al estudio de la interacción de derivados oligoméricos de guanidina bicíclica con sistemas biológicos de gran relevancia, concretamente con el dominio de tetramerización de p53 (p53TD) y determinadas secuencias consenso de ADN, además de explorar su potencialidad como vectores no-proteicos de internalización celular. Los tres últimos capítulos de este trabajo doctoral versan sobre la capacidad que tienen las guanidinas bicíclicas para auto-ensamblarse formando complejos supramoleculares con diferentes compuestos oxoaniónicos y las propiedades físico-químicas derivadas de esa unión
Nature frequently uses guanidinium group (mainly found in the amino acid arginine) to bind via ion pairing and hydrogen bonding different anions (mostly oxoanions), thus facilitating interactions between different macromolecules. This manuscript is divided into two clearly defined sections. The first one is based on the development of a robust and reliable synthetic methodology for the construction of bicyclic guanidinium oligomers of different lengths and functionalization degree and the study of the binding properties of these oligoguanidinium compounds with biologically relevant molecules such as p53 or targeted DNA sequences. Attributable to their cationic nature and hence similarity with cell penetrating peptides, bicyclic guanidinium oligomers were also explored as cell membrane carriers. The second part explores the self-assembly of bicyclic guanidines for calix[4]arene complexation and expansion of their cavities, multiporphyrin-fullerene dyad arrays, and their properties and potential applications as organogelators.

Les hémicryptophanes, molécules constituées d’une unité cyclotriveratrylène (CTV) reliée à un autre groupement de symétrie C3, sont des molécules cages qui trouvent de nombreuses applications dans le domaine de la chimie hôte-invité. Dans une première partie, ce manuscrit présente une revue des développements récents de la chimie des hémicryptophanes et définit les objectifs de ce travail de thèse.Nos travaux concernent principalement le design d'hémicryptophanes spécifiquement conçus pour la reconnaissance moléculaire de substrats d'intérêt. Ainsi, des structures variées d'hémicryptophanes ont été conçues comme capteur fluorescent du phosphate de choline, ou pour la reconnaissance de paire d'ions. Des hémicryptophanes hétéroditopiques originaux portant des unités tris(2-pyridylmethyl)amine (TPA) ont été synthétisés et présentent un grand intérêt pour des applications ultérieures en reconnaissance. Nous avons étudié la reconnaissance stéréosélective de saccharides avec des hémicryptophanes énantiopurs qui associent trois types de chiralité sur sept centres stéréogènes. Enfin, nous décrivons le mouvement de "respiration" moléculaire de cages énantiopures, enrichissant ainsi les rares applications des hémicryptophanes comme machines moléculaires.Des complexes du vanadium(V) des hémicryptophanes ont été développés comme catalyseurs efficaces dans des réactions de sulfoxydation et pour l'oxydation catalytique de lignines. Des dérivés azaphosphatrane d’hémicryptohanes ont été développés comme organocatalyseurs de la réaction de polymérisation par ouverture du lactide. La dernière partie de ce manuscript est consacrée à des développements nouveaux dans le domaine de la formation de cages par auto-assemblage. Nous avons réussi à former par coordination des tétraèdres dont les quatre faces comportent une sous-unité azaphosphatrane. Nous montrons pour la première fois que dans ce type de cage l’unité azaphosphatrane joue un rôle prépondérant dans la complexation d’anions
In the wide area of host-guest chemistry, hemicryptophanes, a type of molecular cages combining a cyclotriveratrylene (CTV) unit with another different C3 symmetrical moiety, have received increasing attention. In a first part of this work, the advances in hemicryptophane chemistry have been thoroughly reviewed and the objectives of the thesis have been postulated. Our work mainly concerns the targeted molecular recognition by rational design of hemicryptophanes. Various hemicryptophane structures have been designed as fluorescent sensors for choline phosphate, or for ion-pairs recognition. Original heteroditopic hemicryptophanes bearing tris(2-pyridylmethyl)amine (TPA) units have been synthesized that present a great interest for further applications in molecular recognition. We investigated the stereoselective recognition of carbohydrates using enantiopure hemicryptophanes combining three classes of chirality on seven stereogenic units. At last, we described the breathing motion of a series of enantiopure cages, complementing the rare application of hemicryptophanes as molecular machines.Hemicryptophane vanadium(V) complexes, have been developed as efficient supramolecular catalysts for sulfoxidation and for the catalytic lignin oxidation. Azaphosphatrane-functionalized hemicryptophanes were developed as hydrogen-bonding organocatalysts for the ring-opening polymerization of lactide. Finally, my attention has opened to a more prospective view focusing on cages constructed by self-assembly, and we have demonstrated the feasibility of introducing azaphosphatrane moieties into tetrahedron capsules using subcomponent self-assembly, and also proved for the first time the utility of azaphosphatranes as anion binding moieties

Understanding the supramolecular interactions governing the self-assembly of molecular building blocks upon surfaces is fundamental to the design of new devices such as sensors or catalysts. Successful heterogeneous enantioselective catalysts have relied upon the adsorption of ‘chiral modifiers’, usually chiral amino acids, onto reactive metal surfaces. One of the most researched examples is the hydrogenation of β-ketoesters using nickel-based catalysts. The stability of the chiral modifiers upon catalyst surfaces is a major obstacle to the industrial scale-up of this reaction. In this study, the replacement of conventional modifiers with porous, chiral and functionalised self-assembled networks is investigated. Perylene-3,4,9,10-tetracarboxylic diimide (PTCDI) and melamine (1,3,5-triazine,-2,4,6-triamine) have been shown to form hydrogen bonded networks on Ag-Si(111)√3x√3R30° in ultra-high vacuum (UHV) and Au(111) substrates in UHV and ambient conditions, these networks are capable of hosting guest molecules. These networks are investigated further in this study. In UHV, the behaviour of the components and network formation on Ni(111) is probed using scanning tunnelling microscopy (STM) and temperature-programmed desorption (TPD). The stability of the PTCDI-melamine network on Au(111) was analysed using TPD. Metal coordination interactions between each of the network components and nickel upon the Au(111) surface were examined by STM before testing the ability of the network to act as a template for metal growth. Finally, a number of polymerisation reactions are investigated with a view to replacing chiral modifiers with porous, chiral, functionalised covalent networks. Periodic covalent networks should possess the greater chemical and thermal stability required for more widespread use. In UHV and ambient conditions, STM is used to monitor the progress of surface-confined reactions on Au(111) and characterise the resultant covalent structures.

Coordination-driven self-assembly has led to the realization of an increasing number of elegant and sophisticated functional structures, the structural complexity of which would be difficult to achieve using conventional covalent chemistry. The synthesis of three-dimensional coordination capsule-like structures is of particular interest due to their multiple potential applications, particularly their use in selective molecular recognition (host-guest chemistry), reactivity modulation (nanoreactors), molecular sensors or biological applications. The main goal of this doctoral thesis, performed in the QBIS-CAT group from the University of Girona, is the preparation of coordination nanocapsules of different sizes (1 and 2) and their application in the selective recognition of specific molecular substrates. On one hand, the smaller capsule (1) displays high selectivity towards anionic, planar-shaped -guests, whilst on the other hand, the larger nanocapsule (2) is able to encapsulate fullerenes in a rapid manner at room temperature, by simply soaking a solid sample of the capsule in a fullerene containing solution. Strikingly, the larger nanocapsule is shown to be effective for the selective separation of C60 from a mixture of fullerenes using a straightforward washing protocol of a solid sample of fullerene containing nanocapsule. Nowadays, the applications of fullerenes (i.e. in solar cells or in medicine) are limited in origin by their purification which is often tedious and expensive. The results of this investigation may pave the way for the future development of new methodologies for the purification of fullerene mixtures. Finally, the confined inner cavity of the larger nanocapsule, 2, was used to encapsulate a chiral rhodium catalyst which gave amongst the highest selectivities in the asymmetric hydroformylation of styrene for a monoligated rhodium catalyst. The results obtained demonstrate a substantial increase in stereoselectivity upon encapsulation of the catalyst, providing evidence of a selectivity-inducing effect by the secondary coordination sphere reminiscent of enzymatic active sites.
La química d’autoacoblament dirigida per enllaços de coordinació ha facilitat l’obtenció d’una gran varietat d’estructures químiques molt sofisticades, la complexitat de les quals hagués estat molt difícil d’aconseguir mitjançant la convencional química covalent. La síntesis de càpsules de coordinació tridimensionals rep un interès especial degut a la multitud d’aplicacions que aquestes ofereixen, destacant la seva aplicació en el reconeixement selectiu de molècules (química receptor-substrat), modulació de la reactivitat (nanoreactors), sensors moleculars o les seves aplicacions biològiques. El principal objectiu d’aquesta tesi doctoral, que ha estat realitzada al grup QBIS-CAT de la Universitat de Girona, és la preparació de nanocàpsules de coordinació de diferents mides (1 i 2), i la seva aplicació en el reconeixement selectiu de substrats moleculars específics. Per una banda, la nanocàpsula més petita (1) és altament selectiva per substrats plans, aniònics amb sistemes . Per altra banda, la nanocàpsula de majors dimensions (2) pot encapsular ful·lerens de manera ràpida i a temperatura ambient, simplement amarant una mostra sòlida de la nanocàpsula en una dissolució de ful·lerens. A més, la nanocàpsula més gran es va emprar amb èxit en la separació selectiva de C60 d’una barreja de ful·lerens utilitzant un senzill protocol experimental basats en rentats del sistema nanocàpsula-ful·lerè en estat sòlid. Actualment, les aplicacions dels ful·lerens (ex. en cel·les solars o en medecina) es veuen limitades per la purificació d’aquestes molècules, que generalment s’aconsegueix mitjançant processos tediosos i costos. Els resultats d’aquesta investigació podrien facilitar el desenvolupament de noves metodologies per la purificació de barreges de ful·lerens. Finalment, la cavitat interior de la nanocàpsula de majors dimensions, 2, es va utilitzar per encapsular un catalitzador de rodi quiral que va donar alts valors de selectivitat, dels més alts que s’han observat per a un catalitzador de rodi monolligat. Els resultats obtinguts demostren que l’encapsulació del catalitzador incrementa notablement l’estereoselectivitat de la reacció, i indiquen que el confinament del catalitzador dins la caixa causa un efecte d’inducció de la selectivitat similar al que té lloc en els centres catalítics dels enzims.

Dans cette thèse, nous avons étudié les propriétés photoniques et vibrationnelles de monocouches moléculaires auto-assemblées sur graphène et la possibilité d'utiliser des multicouches auto-assemblées de pérylène comme milieu à gain pour l'amplification de plasmons. Le graphène, en tant que matériau transparent et conducteur, a permis pour la première fois de corréler la géométrie du réseau de l’auto-assemblage supramoléculaire avec ses propriétés optiques, grâce à la microscopie à effet tunnel et à des mesures de spectroscopiques optiques et Raman. En comparant plusieurs colorants autoassemblés sur le graphène, nous avons mis en lumière les effets des interactions intermoléculaires et des interactions colorant-graphène sur le spectre d'absorption du colorant adsorbé. Le transfert d'énergie rapide des colorants vers la couche degraphène par les mécanismes de Förster et de Dexter empêche toute relaxation radiative du colorant..Néanmoins, nous avons démontré la première fonctionnalisation fluorescente non-covalente du graphène par une monocouche de colorants autoassemblée en mettant en place une stratégie à base d’espaceurs. Nous avons exploité l’extinction rapide de la fluorescence des colorants par le graphène pour étudier les spectres Raman des auto-assemblages moléculaires sur graphène, et nous avons révélé l'apparition d'un mode vibrationnel couplé entre les molécules adsorbées et le substrat de graphène. Nous avons démontré le régime de couplage fort entre un auto-assemblage tri-dimensionnel de pérylène et un plasmon polariton de surface en optimisant l'orientation et l'organisation des molécules de colorant par rapport au champ électrique du mode de plasmon. Nous avons prouvé que les milieux de gain auto-assemblés en agrégats-J peuvent théoriquement conduire à des milieux de gain efficaces pour l'amplification de plasmons. Cependant, nous avons révélé expérimentalement que les recombinaisons exciton-exciton limitent le taux de pompage à des fluences élevées dans ces milieux denses
In this work, we have studied thephotonic and vibrational properties of selfassembled molecular monolayers on graphene and the possibility to use perylene self-assembled multilayers as a gain medium for plasmon amplification. Graphene, as a transparent and conductive material, has offered for the first time to correlate the self-assembly structure as deduced from scanning tunneling microscopy to photonic properties as analyzed by optical and Raman spectroscopy measurements. By comparing several self-assembled dyes on graphene we have shed lighton how intermolecular and dye-graphene interactions modify the absorption spectrum of the adsorbed dye.Fast Förster and Dexter energy transfer from the adsorbed dyes to the graphene layer prevent any radiative decay of the dye.Nevertheless, we have demonstrated the first fluorescent non-covalent functionalization of graphene by a supramolecular self-assembled monolayer using a spacer approach.We have exploited the fast dye fluorescence quenching by graphene to study Raman spectra of self-assembled dye on graphene, and we have shown the appearance of a coupled vibrational mode between the adsorbed molecules and the graphene substrate. We have demonstrated the strong couplingregime between a three-dimensional perylene self-assembly and a propagating plasmon polariton by optimizing the orientation and the organisation of the dye molecules compared to the electric field of the plasmon mode. We have shown that J-aggregated self-assembled gain media may theoretically lead to efficient gain media for plasmon amplification. However, we experimentally demonstrated that exciton-exciton recombination limits the achievable pumping rate at high fluences in such dense media

In der vorliegenden Dissertation werden das Selbstaggregationsverhalten und die elektronischen Eigenschaften von vier expandierten pi-konjugierten Makrozyklen in geordnete supramolekulare Architekturen mit Hilfe von Rastertunnelmikroskopie (STM) und Tunnelspektroskopie (STS) an Fest-Flüssig-Grenzflächen zwischen organischen Moleküllösungen und der Basalfläche von Graphit untersucht. Zwei Makrozyklen sind die Fotoisomere Z,Z–8T6A und E,E–8T6A, in denen sechs Ethynylengruppen und zwei cis- bzw. trans-Ethylen erhalten sind. STM-Bilder zeigen 2-dimensionale hexagonale Gitter. Strom-Spannungs-Kennlinien bestätigten den erwarteten donor-artigen Charakter der Makrozyklen. Das Schalten von Z,Z–8T6A zu E,E–8T6A wird durch STS zyklische Messungen angezeigt, nachdem die stabilste kationische Spezies ausgebildet wurde. Diese Ergebnisse stellen das erste elektrochemische Schalten unter Standard STM Bedingungen dar. Außerdem wurden die Photoisomerisierungen zwischen Z,Z-8T6A und E,E-8T6A an der Fest-Flüssig-Grenzfläche beobachtet. Eine selbstorganisierte Monoschicht aus Wasserstoffbrücken-gebundenen Trimesinsäuren an der Fest-Flüssig-Grenzfläche bildet Wirtsstellen für die epitaktische Anordnung von Fullerenen mit E,E–8T6A Komplexen in Mono- und Doppelschichten aus. Mit Hilfe der STM-Tomographie wird die Bildung der Templatschicht überprüft. Die Konformationsstabilität und die Adsorptionsstellen der Monoschichten werden mit der Hilfe von Molekulardynamik-Simulation bestätigt. Die STS-Experimente zeigen die Modifikation der gleichrichtenden Eigenschaften der Makrozyklen durch die Bildung von Donor-Akzeptor-Komplexen in einer dicht gepackten, selbstorganisierten supramolekularen Nanostruktur. Die Kombination von Wirt-Gast-Komplexen mit der Schaltfähigkeit und den elektronischen Transporteigenschafte von makrozyklischen Oligothiophenen prädestinieren diese als Kandidaten für Anwendungen in supramolekular konstruierten Systemen mit gewünschten (opto)elektronischen Eigenschaften.
The present thesis concerns to the self-assembly and the electronic properties of four pi-expanded macrocycles into ordered supramolecular architectures, investigated by means of scanning tunneling microscopy (STM) and spectroscopy (STS) at the solid-liquid interface between organic solutions and the basal plane of graphite. Two macrocycles are the photoisomers Z,Z–8T6A and E,E–8T6A, which contain six ethynylenes and two cis- and trans-ethylenes in opposite positions of the ring, respectively. STM images reveal hexagonally ordered 2D-networks. Current–voltage characteristics confirm the expected donor-like character of the macrocycles. Cyclic STS measurements indicate that Z,Z–8T6A switches to E,E–8T6A after formation of a most stable cationic species. This result represents the first reported electrochemical switching experiment under standard STM conditions. Additionally, the reversible photoisomerization between Z,Z-8T6A and E,E-8T6A upon irradiation was recognized at the solid-liquid interface. Moreover, a self-assembled monolayer of hydrogen-bonded trimesic acid at the solid-liquid interface provides host-sites for the epitaxial ordering of Saturn-like complexes of fullerenes with E,E–8T6A macrocycles in mono- and bilayers. STM tomography verifies the formation of the templated layer, while molecular dynamics simulations corroborate the conformational stability and assign the adsorption sites of the adlayers. STS measurements reveal the modification of the rectifying properties of the macrocycles by the formation of donor-acceptor complexes in a densely packed all-self-assembled supramolecular nanostructure. The combination of host-guest complexation and the switching capabilities and electronics transport characteristics of cyclic oligothiophenes render them candidates for applications in the study of supramolecular engineered systems with desirable (opto)electronic properties.

2013/2014
Artificial molecular structures forming stable pores in biological membranes may have important applications in the biomedical field and in the field of biotechnology, in particular as sensors. These structures have to meet specific characteristics of size, shape and solubility. In particular, they have to enter the membrane engaging hydrophobic interactions with the phospholipid bilayer and, at the same time, forming a polar conduit for the transport of the ions across the membrane. A molecular structure which meets these features is an amphipathic, rigid and tube-shaped one and, mostly important, long enough to span the entire membrane. The final goal of this thesis work is the design and preparation of structures that would reflect these characteristics obtained by the metal-mediated self-assembly of pyridylporphyrins. In particular to obtain structures long enough to span the membrane the focus was on the design of pyridylporphyrins equipped with complementary hydrogen bonding donor/acceptor moieties and of a polar subunit to increase membrane compatibility. Using transition metal complexes with an adequate geometry these “molecular panels” should self-assemble in metallasquares which, upon hydrogen-bonding driven dimerization in membrane, should form tubular empty structures long enough to span the phospholipid bilayer forming large pores. In the first part of the Thesis work, a versatile and straightforward synthetic strategy for the preparation of a library of amphiphilic trans-A2B2 and trans-A2BC dipyridylporphyrins directly from 5-(4-pyridyl)dipyrromethane has been developed and optimized. The major part of the porphyrins synthesized in this way are new compounds.The library members have been functionalized through different metal catalysed coupling reactions, showing their great potential and versatility towards the different employment which could be addressed, to obtain amphiphilic and dimeric derivatives, in some cases with very good and satisfying yields. The derivatization reactions have been performed on the free base porphyrins and, therefore, it has been necessary to carefully optimize the conditions of the metal catalysed reactions in order to avoid the insertion of the catalyst, or of the co-catalyst, in the porphyrin macrocycle. The functionalities that have been inserted into the dipyridylporphyrins scaffold are hydrogen-bonding complementary donor/acceptor moieties, like uracil and diacylaminopyridine, and an amphiphilic polyether chains. Starting from the porphyrin library and exploiting metal catalysed coupling reaction also three dipyridylporphyrins dimers have been prepared. The target amphiphilic dipyridylporphyrins have been principally utilized in self-assembly reactions exploiting the pyridyl groups present, in particular through the coordination-driven self-assembly approach, with cis-coordinating metal complexes like Re(CO)5Br and trans,cis,cis-[RuCl2(CO)2(DMSO-O)2], leading to the formation of molecular squares together with other kind of metallacyclic species. At the best of our knowledge, this is the first time that the Ru(II) complex have been employed for the self-assembly with trans-dipyridylporphyrins. The porphyrins, the dimers and supramolecules synthesized have been mainly characterized by mean of NMR spectroscopy, in particular through 1H, 13C, 1H-1H COSY, 1H-13C HSQC, 1H-DOSY. The latter technique, being more and more important and utilized in supramolecular chemistry either in the characterization either in the sample purity proof of the compounds, has been in fact thoroughly utilized both to confirm the dimensions in solution of all the molecules synthesized and to give an evidence of their purity. This last feature has been one of the more challenging to face because the sample purity was not so evident just analysing the 1H-NMR spectra due to the possible presence of isomers and conformers. In absence of X-ray spectroscopic and MS spectrometric data, PFG-NMR has been a powerful, helpful and straightforward way to rationalize the high complexity of the resonating signals pattern in these spectra and to confirm the higher molecular dimensions reached as relative to the parent porphyrins. Confirmation of the pyridyl-metal bond formation with the right configuration has come also from IR, UV-Vis and fluorescence emission spectra acquired both for the porphyrins and for the supramolecular metallacycles. Putting together all the data and although in some cases we were not able to unambiguously define the nuclearity of the metallacycle, the supramolecules synthesised have all cyclic and symmetric structure and retain the symmetry of their parent porphyrins.The most representative porphyrins, together with the supramolecular metallacycles have been then tested as transmembrane ion channels utilizing liposomes as model of biological membranes. Preliminary studies on the H+ transport assays have been reported.
Le strutture molecolari artificiali capaci di formare nanopori stabili all’interno di una membrane biologica sono sempre più di ampio interesse, grazie alla possibilità di essere impiegate in campo biomedico e biotecnologico, soprattutto come sensori. Per poter formare nanopori questi sistemi devono soddisfare dei requisiti minimi in termini di forma, dimensioni e solubilità. Essi devono essere in grado di inserirsi facilmente in membrana tramite interazioni idrofobiche e al contempo formare condotti polari che consentano il passaggio degli ioni; quindi una struttura che presenti tali caratteristiche dovrà essere anfifilica, avere una forma allungata, essere abbastanza rigida e, soprattutto, essere sufficientemente lunga da attraversare completamente la membrana. Lo scopo di questo lavoro di tesi è quello di realizzare sistemi che soddisfino queste esigenze sfruttando il metal-mediated self-assembly di piridilporfirine su centri metallici. In particolare, per ottenere strutture sufficientemente lunghe da attraversare completamente il doppio strato fosfolipidico, si è focalizzata l’attenzione sulla realizzazione di piridilporfirine equipaggiate con gruppi accettori e donatori di legami ad idrogeno e con un catena anfifilica che ne aumenti la compatibilità con la membrana. Utilizzando complessi di metalli di transizione con una geometria adeguata questi “pannelli molecolari” dovrebbero assemblarsi a dare metallacicli di forma approssimativamente cubica in grado di dimerizzare in membrana, grazie alla formazione di legami ad idrogeno, formando così strutture tubulari cave sufficientemente lunghe da attraversare completamente la membrana. Nella prima parte della Tesi è stata messa a punto ed ottimizzata una strategia sintetica per ottenere una libreria di derivati anfifilici di trans-A2B2 e trans-A2BC dipiridilporfirine direttamente a partire dal 5-(4-piridil)dipirrometano. La maggior parte delle porfirine sintetizzate in questo modo sono composti nuovi. I membri della libreria sono stati quindi funzionalizzati attraverso reazioni di coupling metallo-catalizzate per ottenere sia derivati anfifilici che dimerici, dimostrando così il loro potenziale e la loro versatilità verso l’utilizzo per diverse applicazioni. Le reazioni di funzionalizzazione sono state condotte sulle porfirine free-base ed è stato dunque necessario ottimizzare accuratamente le condizioni delle reazioni metallo-catalizzate in modo tale da evitare che il catalizzatore, o l’eventuale co-catalizzatore, si potesse inserire nel macrociclo porfirinico. Le funzionalità che sono state inserite nelle dipiridilporfirine sono molecole con gruppi donatori/accettori di legame idrogeno tra di loro complementari , in particolare, derivati dell’uracile e della diacilamminopiridina, e residui anfifilici come catene polieteree. Partendo dalla libreria di porfirine sono anche stati sintetizzati dei dimeri di dipiridilporfirine. Le dipiridilporfirine target sono state principalmente utilizzate in reazioni di auto-assemblaggio sfruttando i gruppi piridinici presenti, in particolare attraverso il metodo coordination-driven self-assembly con complessi metallici cis-coordinanti come Re(CO)5Br e trans,cis,cis-[RuCl2(CO)2(DMSO-O)2], ottenendo la formazione di quadrati molecolari insieme con altre specie metallacicliche. Al meglio delle nostre conoscenze, il complesso di Ru(II) è stato utilizzato per la prima volta per l’auto-assemblaggio con trans-dipiridilporfirine. Le porfirine, i dimeri e gli addotti supramolecolari ottenuti sono stati caratterizzati principalmente tramite spettroscopia NMR, in particolare attraverso 1H, 13C, 1H-1H COSY, 1H-13C HSQC, 1H-DOSY. Quest’ultima tecnica, essendo divenuta sempre più importante in chimica supramolecolare sia per la caratterizzazione sia per provare la purezza dei composti, è stata utilizzata a fondo per confermare le dimensioni in soluzione delle molecole sintetizzate e per avere una prova della purezza dei campioni. Quest’ultimo aspetto è stato uno dei più difficili da affrontare perché non era certo evidente analizzando i soli spettri 1H-NMR acquisiti per la possibile presenza di isomeri e confomeri. In assenza di dati spettroscopici a raggi X e di spettrometria di massa, la tecnica PFG-NMR è stata uno strumento potente, utile e diretto per razionalizzare l’elevata complessità del pattern dei segnali osservato in questi spettri e per confermare le più elevate dimensioni raggiunte da queste molecole relativamente alle porfirine di partenza. Conferma dell’avvenuta formazione dei legami metallo-piridina con la giusta configurazione è venuta anche dai dati spettroscopici IR, UV-Vis e di emissione di fluorescenza, acquisiti per le porfirine così come per i metallacicli supramolecolari. Anche se non è stato possibile in alcuni casi assegnare in maniera non ambigua la nuclearità di queste supramolecole, poiché la geometria molecolare sia di specie a nuclearità [3+3] che [4+4] può essere approssimata dalla medesima sfera, le supramolecole sintetizzate sono specie cicliche e simmetriche e preservano la simmetria molecolare delle specie di partenza.Le porfirine più rappresentative e gli addotti metallaciclici sono stati testati per la loro capacità di formare canali ionici transmembrana utilizzando liposomi come modelli delle membrane biologiche. Gli studi preliminari sull’attività di trasporto di ioni H+ sono riportati nella Tesi.
XXVII Ciclo
1982

La investigación realizada en esta tesis se ha basado en la síntesis y estudio de propiedades de arquitecturas 2D y 3D autoasociadas. En este contexto, derivados de ciclotriveratrileno (CTV) triplemente funcionalizados con unidades de ureidopirimidinona dieron lugar a capsulas autoasociadas capaces de incluir fulerenos de diferente tamaños (C60, C70 y C84) en su interior. La diferencia de estabilidad de los diferentes complejos permitió el desarrollo de una nueva metodología para purificar fulerenos. Basado en este diseño, se sintetizaron también carcerandos los que el fulereno queda atrapado permanentemente en la cavidad. La metodología de Grubbs permitió la unión covalente de las dos hemicapsulas. Además, se han desarrollado nuevos receptores para fulerenos usando unidades cóncavas como el CTV funcionalizados con tres tetratiafulvalenos extendidos. Estos complejos presentaron propiedades interesantes para el desarrollo de nuevos materiales para dispositivos fotovoltaicos. Finalmente, se investigó la síntesis de agregados cíclicos bidimensionales basados en bis-UPys disimétricas con el objetivo de crear nuevo materiales porosos organizados
The research of this thesis has been based on the synthesis and the study of the properties of self-assembled 2D and 3D architectures. In this contex, cyclotriveratrylene (CTV) derivatives triply functionalized with ureidopyrimidinone (UPy) units were synthesized. They self-assemble into a capsule large enough to include fullerenes of different sizes such as C60, C70 or C84. Taking advantage of the stability differences between the complexes, a new methodology for fullerene purification has been developed. Besed on the previous design, carcerands that permanently entraps fullerenes were synthesized using Grubbs methodology to covalently link both hemicapsules. In addition, a new kind of fullerene receptors using the concave surface of the CTV scaffold, endowed with three units of extended tetrathiafulvalene were(exTTF), were studied. These complexes display interesting properties to develop new materials in the field of photovoltaic devices. Finally, the synthesis of cyclic 2D aggregates based on dissymmetric bis-UPys was investigated with the aim of creating new organized porous materials.

Dans ce manuscrit est décrite l'utilisation d'interactions supramoléculaires pour diriger l'auto-assemblage de composés donneurs et accepteurs d'électrons au sein de dispositifs photovoltaïques organiques. Dans ce but, des matériaux de type oligo-3-hexylthiophène et fullerène ont été fonctionnalisés avec des groupements de reconnaissance complémentaires mélamine – acide barbiturique. La présence de élements solubilisants confère à ces composés une bonne mise en oeuvre permettant la fabrication de dispositifs photovoltaïques à hétérojonction volumique. L'effet de la composition et du post-traitement de la couche active sur la performance de ces dispositifs ont été explorés. Les études de mobilité de charge et des mécanismes de recombinaison au sein de ces matériaux indiquent que l'équilibre entre auto-association et séparation de phases est crucial pour l'efficacité en conversion photovoltaïque
This research aims to elucidate the use of supramolecular interaction to guide the formation of well-defined nanoscale self-assembled architecture in photovoltaic solar cells as a means to improve device efficiency. Complementary molecular recognition sites based on melamine and barbituric acid were used to obtain functionalized fullerene and oligothiophene materials with superior processibility thanks to the presence of specific solubilizing groups. The efficiency of solid-state devices fabricated using the bulk heterojunction design was studied with respect to device morphology and composition. Experiments on recombination mechanism and field effect mobilities suggest that the balance between hydrogen-bonding interactions induce self-assembly and p-p interactions to promote phase segregation is crucial to the micro-structure of the active layer. The investigated of the relationship between the oligothiophene chain size and various complementary hydrogen-bonding motifs is envisaged

The self-assembly of structured particles into monodisperse clusters is a challenge on the nano-, micro- and even macro-scale. While biological systems are able to self-assemble with comparative ease, many aspects of this self-assembly are not fully understood. In this thesis, we look at the strategies and rules that can be applied to encourage the formation of monodisperse clusters. Though much of the inspiration is biological in nature, the simulations use a simple minimal patchy particle model and are thus applicable to a wide range of systems. The topics that this thesis addresses include: Encapsulation: We show how clusters can be used to encapsulate objects and demonstrate that such `templates' can be used to control the assembly mechanisms and enhance the formation of more complex objects. Hierarchical self-assembly: We investigate the use of hierarchical mechanisms in enhancing the formation of clusters. We find that, while we are able to extend the ranges where we see successful assembly by using a hierarchical assembly pathway, it does not straightforwardly provide a route to enhance the complexity of structures that can be formed. Pore formation: We use our simple model to investigate a particular biological example, namely the self-assembly and formation of heptameric alpha-haemolysin pores, and show that pore insertion is key to rationalising experimental results on this system. Phase re-entrance: We look at the computation of equilibrium phase diagrams for self-assembling systems, particularly focusing on the possible presence of an unusual liquid-vapour phase re-entrance that has been suggested by dynamical simulations, using a variety of techniques.

2011/2012
In the last years, gold nanoparticles (AuNPs) protected by an organic shell of ligands have received a large interest for applications in the biomedical field in particular for diagnosis, imaging and therapy. This class of nanomaterials is largely used because of the easy of synthesis with different core sizes and shapes and controlled dispersion. Moreover, NPs can be protected by a large variety of organic compounds, with different functionalities and to allow the linkage of drugs and biomolecules. The nature of the ligand is responsible of the solubility of the NPs and could be also tuned in order to have NPs soluble in water and in the biological environment. Additionally, at least gold is no toxic, biocompatible and could be easily released from the body. The present thesis is focused on three projects. The first one deals with the study of the morphology of gold nanoparticles coated by a mixture of hydrogenated and fluorinated ligands which solubility in water is favored by the presence of PEG chains. Few years ago, our research group has shown that mixtures of these hydrogenated and fluorinated ligands, forming the monolayer of gold nanoparticles, phase-segregate in separated domains because of the reciprocal immiscibility of the two chains. During this thesis, we wanted to investigate more deeply the organization of such monolayers and in particular, to understand the shape and the size of these domains. In collaboration with the group of Prof. S. Pricl and Prof. M. Fermeglia of the University of Trieste, in silico experiments have been performed in order to predict the size and the shape of these domains. Moreover, we have studied how the shape and the size of these domains is influenced by the ratio between the two thiols, the size of the core and the difference in length between the two ligands. The obtained results were supported by further ESR experiments performed by Prof. Lucarini of the University of Bologna. ESR experiments have allowed us to estimate the value of the affinity constants of the probe for the fluorinated and hydrogenated domains of the monolayer and to establish that mixed monolayers have chemical and physical properties that cannot be predicted by simply knowing the properties of homoligand monolayers. The results that have been reported in a recent publication on ACS Nano are presented in Chapter 3. The second project of this PhD thesis is based on the synthesis and characterization of water soluble gold nanoparticles coated by different ratios of charged hydrogenated ligands and commercially available fluorinated ligands. Some of these nanoparticles, with an average core diameter between 3 and 4 nm, have been used for preliminary investigations in vitro. In particular, cell membrane permeation and the cellular toxicity have been evaluated. These experiments have been performed in collaboration with the group of Prof. Stellacci in IFOM-IEO, Milan. Preliminary results are described in Chapter 4. The last part of this PhD project is focused on the synthesis and characterization of NPs coated by mixtures of commercially available fluorinated and hydrogenated thiols. These NPs present the advantages over those described in Chapter 3 and Chapter 4 because they are suited for a direct “visualization” by STM experiments and may help us in understanding the rules governing the organization of mixtures of fluorinated and hydrogenated ligands on a curved surface. The choice to synthesize NPs without charged groups is dictated by the limitations of STM technique. In Chapter 5 synthetic aspects and preliminary STM results would be presented.
XXV Ciclo
1983

The present thesis work dealt with the study of the polar interiors of self-assembled homocapsules based on aryl-extended calix[4]pyrrole scaffolds, as well as the anisotropic polar interior of a mechanically locked calix[4]arene-calix[4]pyrrole heterocapsule. The properties of the internal cavities of the receptors were probed through the inclusion of different molecules known as guests. Homologous series of aliphatic N-oxides were used in encapsulation experiments to evaluate the size modification and adaptability exhibited by the aromatic cavity enclosed in both systems. Moreover, new super aryl-extended calix[4]pyrroles were synthesized by the elongation of the aromatic walls of aryl-extended calix[4]pyrroles yielding a substantial increased volume of the internal cavity. Additionally, the preparation of an unprecedented calix[4]pyrrole – calix[4]pyrrole molecular container having the two hemispheres mechanically linked was achieved. This capsule features a sizeable increase of its internal volume when compared to the previous calix[4]arene-calix[4]pyrrole molecular container. Both mechanically locked capsules displayed a bis-[2]-catenane topology. Furthermore, the new mechanically locked homo-dimer possesses polar functionalization at the closed ends of both hemispheres.
En la presente tesis se han estudiado las cavidades polares de cápsulas autoensambladas basadas en estructuras de calix[4]pirrolesaril-extendidos, así como también las cavidades de cápsulas formadas por dos hemisferios distintos, uno de calix[4]areno y otro de calix[4]pirrol que se encuentran mecánicamente entrelazados, mediante la encapsulación de distintos tipos de moléculas a las cuales llamamos huéspedes. Series homólogas de N-óxidos alifáticos se utilizaron en los experimentos de encapsulación para evaluar la modificación del tamaño de cavidad y la adaptabilidad exhibida por la cavidad aromática en los dos sistemas capsulares. Además, se ha sintetizado nuevoscalix[4]pirroles super extendidos mediante la elongación de las paredes aromáticas de los anteriormente conocidoscalix[4]pirroles aril-extendidos, lo que ha repercutido en un considerable incremento del volumen de interno de la cavidad. Asimismo, se ha logrado sintetizar un contenedor molecular basado en dos moléculas de calix[4]pirroles en el cual los dos hemisferios están mecánicamente unidos, del mismo modo que lo estaban en la anterior cápsula formada por un calix[4]areno y un calix[4]pirrol. La obtención de esta nueva cápsula molecular ha supuesto un aumento de volumen con respecto a la anterior cápsula también enlazada mecánicamente. Los dos contenedores moleculares descritos presentan una topología de bis-[2]-catenano. La nueva cápsula molecular posee una funcionalización polar interior en los dos hemisferios, una diferencia con respecto a la anterior.

2009/2010
“There is plenty of room at the bottom”. These were the famous words of Richard P. Feynman in 1959 that led to the birth of nanotechnology and nanoscience. Electronic devices based on inorganic semiconductors have been part of our daily lives for the last 60 years. Their miniaturisation has occurred gradually over the years, however, according to Moore’s law the contemporary microelectronic industry’s “top-down” manufacturing technique will soon reach its limits. Therefore, the recent development and increased knowledge of organic semiconductors has led to a tendency to explore alternative avenues with a focus on the creation of electronic devices based on organic molecules. The invention of techniques such STM (1981) and AFM (1986) have facilitated this research, allowing the imaging and manipulation of surfaces and molecules at the nanometre scale (0.1-100 nm). The next step is therefore the development of methods for the controlled fabrication of molecular assemblies and their integration into usable macroscopic systems. In this respect, the “bottom-up” approach offers considerable advantages over any other methodology (i.e. “top-down”) for the construction of nanoscale functional materials and devices. This approach generally exploits the hierarchical self-assembly of functional molecules through multiple non-covalent interactions to prepare long range ordered and defect-free assemblies barely accessible through conventional covalent synthesis. However, an intrinsic drawback of investigating such systems in solution or in a crystal is that molecular components cannot be directly addressed on a nanometric scale. As a consequence, the best engineering methodology involves modifying the surfaces of bulk materials such as metals or semiconductors by deposition of functional organic materials. The modified surfaces are then characterised using scanning probe microscopies (e.g. STM, AFM). To this end, surface-confined, supramolecularly constructed, bi-dimensional (2D) networks, featuring regular porous domains (controllable both in shape and size) are of particular significance in this research domain because their cavities can be used as receptors for the confinement of other remotely controlled functional molecules (e.g. molecular switches, luminescent chromophores). Since these complex nanostructures could ultimately find applications as optoelectronic devices, research efforts in this domain have been gathering momentum in recent years. In Chapter 1, the reader is introduced to the methods employed to construct porous networks on surfaces via supramolecular interactions. The second part of the chapter deals with recent examples of recognition, selection and immobilisation of guest molecules within the cavities of the networks, which is followed in the third part with a discussion about surface assemblies that display structural features or functionality in the third dimension. The last section of the chapter is devoted to the construction of porous networks on surfaces via the interactions of biomimetic molecules (e.g. DNA), which leads to the objectives of the present doctoral project. Inspired by the self-assembly of DNA into nanoporous arrays, it was postulated that the Watson-Crick base pairing of oligonucleotide’s nucleobases would be ideal in preparing 2D porous networks with large receptor cavities. The idea was to covalently attach complementary single stranded oligonucleotides to rigid angular and linear unit core modules respectively, and then allow the two units to self-assemble on surfaces. However, instead of using DNA oligonucleotides, the use of peptide nucleic acid (PNA) oligonucleotides was proposed since more robust architectures would be obtained due to the higher duplex stability displayed by this class of biomimetic molecules. This doctoral dissertation describes the synthetic steps taken towards achieving this goal. The design of the angular and linear units bearing complementary PNA oligomers, required for the preparation of self-assembled nanoporous arrays are described. However, prior to synthesizing these complex molecules, a simpler proof of principle was required to confirm that PNA duplexes could be formed on surfaces and also, whether the presence of chromophoric moieties (e.g. porphyrin) appended to the PNA strands had any effect on duplex formation and duplex stability. The molecule designed for this proof of principle was a self-complementary PNA dodecamer bearing a porphyrin adduct. The synthesis of the self-complementary PNA oligomer required for the preparation of the PNA-porphyrin adduct is described in the first part of Chapter 2. The main synthetic routes and protecting-group strategies used to prepare PNA monomers and oligomers are described first. This is followed by a discussion of the orthogonal protecting group strategies chosen for our project that would allow the isolation of PNA oligomers bearing protected nucleobases following resin-cleavage. This is contrary to the general norm in existing strategies wherein resin-cleavage and nucleobase deprotection is carried out in situ, however, it was required in our synthetic strategy since the terminal amino group of the PNA oligomers was required for further solution phase reactions. To this end, two protecting group strategies were proposed, a Fmoc/Mmt and Fmoc/Cbz-protecting group strategies. The solid support chosen for the Fmoc/Mmt strategy was Tentagel featuring a base-cleavable linker. Due to the failure to hydrolyse the linker during the resin-cleavage step, the Fmoc/Mmt strategy was abandoned. In the second strategy, an acid-cleavable Rink amide resin was chosen as the solid support, therefore a Fmoc/Cbz-protecting group strategy was chosen since it would allow the TFA-mediated cleavage of the oligomer from the resin, without the deprotection of the Cbz groups from the nucleobases. The preparation of the target PNA oligomer (sequence: TTAATTAATTAA) using the Fmoc/Cbz strategy is described in the next section. First, the required monomers for the oligomer synthesis were prepared using established procedures. Then, following reports of the advances in microwave assisted solid phase peptide synthesis claiming improved purity of oligomer products using short coupling times, the solid phase PNA oligomerisation was attempted using microwave irradiation. Three attempts were performed. The first, using a standard laboratory microwave, resulted in a complex mixture of products at the dodecamer stage. An improvement was observed in the results using the CEM discover SPS microwave which was specifically designed for solid phase synthesis, however, the crude dodecamer obtained was still inseparable from the by-products. Similar results were obtained with the CEM liberty microwave, which was an automated solid phase synthesis setup. Finally, utilising manual solid phase synthesis, the target PNA dodecamer was obtained. The HPLC chromatogram of crude PNA dodecamer obtained following resin cleavage displayed a single major product, which was subsequently purified. The oligomer was then deprotected by treatment with TMSI, and was analysed by mass spectrometry, which confirmed that the target dodecamer had been isolated. Section 2.2 described our efforts to prepare PNA-chromophore adducts. Following the isolation of the PNA dodecamer, attempts to covalently attach a porphyrin moiety to the resin-bound oligomer via an amide linkage failed, possibly due to steric hindrance. Subsequently, an azide linker was appended to the oligomer, and attempts to attach an acetylene functionalised porphyrin using a Cu(I)-catalysed 1,3-dipolar cycloaddition were performed. Unfortunately, this approach also did not yield the target adduct. These unsuccessful results paved the way to the development of a Cu(I)-free 1,3-dipolar cycloaddition that enabled the attachment of chromophores to the PNA oligomer. Recently published reports of Cu(I)-free 1,3-dipolar cycloaddition reactions applied on DNA oligomers offered inspiration towards this goal. The reported strategies involved the generation of a nitrile oxide species, which then reacted with either an alkene or an alkyne to form an isoxazoline or an isoxazole. Two methods of generating the nitrile oxide species were evaluated using anthracene derivatives. The first method involved the base-mediated dehydrochlorination of anthracene hydroximoyl chloride to yield the nitrile oxide, which then reacted with a dipolarophile that was introduced into the reaction mixture. The second approach to generating a nitrile oxide species involved treating an O-silylated hydroxamic acid derivative of anthracene with trifluoromethanesulfonic anhydride in the presence of a base (Carreira’s method). Following successful trapping of the nitrile oxides generated by both methods using trimethylsilyl ethylene as the dipolarophile, the reactions were applied on a resin-bound, acetylene-functionalised PNA dodecamer. Both methods yielded the target PNA-anthracene adduct. Since the nitrile oxide-acetylene 1,3-dipolar cycloaddition reaction had never been applied on porphyrins, a method had to be developed. Attempts to prepare a hydroximoyl chloride derivative of a porphyrin resulted in the decomposition of the macrocycle upon treatment with chlorinating agents (NCS, tert-BuOCl, and 1-chlorobenzotriazole), therefore, the hydroximoyl chloride method was abandoned in favour of the Carreira method. An O-silylated hydroxamic acid derivative of porphyrin was synthesized, and upon exposure to trifluoromethanesulfonic anhydride and Et3N, the nitrile oxide was generated and was trapped with a large excess (200 eq.) of trimethylsilyl ethylene yielding the target tetra-isoxazole porphyrin derivative in 62% yield, which corresponded to a yield of 89% per 1,3-dipolar cycloaddition. Optimisation of the reaction conditions using phenyl acetylene as the dipolarophile allowed similar yields to be obtained with only a 10 eq. excess of the acetylene. Having developed a protocol that was compatible with both PNA and porphyrin, the utility of the method to prepare a variety of PNA-chromophore adducts was tested. Hydroxamate derivatives of pyrene, porphyrin, phenanthroline and fluorescein chromophores were prepared. Subsequently, the corresponding nitrile oxide species were generated and were reacted with the resin-bound, acetylene-functionalised PNA dodecamer. The PNA-pyrene adduct was successfully isolated (Figure v), however, the other target PNA-chromophore products were not isolated. The porphyrin nitrile oxide derivative was insoluble in the reaction medium, thus preventing the cycloaddition reaction from proceeding. In the case of the fluorescein hydroxamate, the presence of nucleophilic functional groups in the starting material were probably reactive towards the trifluoromethanesulfonic anhydride reagent, therefore it was unlikely that the nitrile oxide species was formed, and thus the cycloaddition reaction could not proceed. Finally, the reaction with the phenanthroline derivative yielded a new product, however mass spectrometry analysis indicated that it did not correspond the target PNA-phenanthroline adduct. Further work is currently underway to re-evaluate these reactions. In parallel to the synthetic work, a preliminary study into the deposition of PNA onto mica surfaces was investigated using AFM imaging. Deposition of drops of an aqueous solution of deprotected self-complementary PNA dodecamer onto clean mica surfaces using spin coating resulted in aggregates of PNA on the surface. Following annealing of the solution, a repeated deposition of a single drop of the solution resulted in a completely different surface assembly. The surface was saturated by what was thought to be PNA duplexes. This was confirmed by the deposition of drop of a solution that was diluted ten-fold which resulted in an AFM image where bright spot were intermitted by clean mica surface. Topographical analysis of the surface indicated that the bright spots were an average in 1 nm in height, which closely corresponds to the expected height of PNA duplexes, thus confirming that PNA duplexes could be deposited onto surfaces.
XXII Ciclo
1981

L'objectif de ces travaux est la synthèse molécules destinées à la formation de fils moléculaires par auto-assemblage. La reconnaissance sélective d'un noyau imidazole par une porphyrine de zinc à anse phénanthroline est utilisée comme outil pour l'assemblage. Plusieurs variations structurales ont été apportées aux blocs d'assemblage de manière à explorer différentes possibilités de contrôle sur la formation des fils moléculaires. Sont présentés dans ce document, les synthèses des molécules, ainsi qu'une partie des études réalisées pour interpréter la nature des assemblages formés à la fois en solution, mais également sur des surfaces. La microscopie à force atomique a mis en évidence des espèces linéaires régulières auto-assemblées dont la formation est assistée par la surface.

Das grundlegende Verständnis der Adsorption, der Eigenschaften, und der Wechselwirkungen von komplexen organischen Molekülen auf Festkörperoberflächen ist für die Entwicklung neuer Anwendungen in der Nanotechnologie von entscheidender Bedeutung. Die in dieser Arbeit untersuchten funktionellen Bausteine gehören zu den Porphyrinen und Phthalocyaninen. Deren Adsorption, elektronische Struktur, und Reaktionen der Moleküle auf Edelmetalloberflächen wurden mit mehreren Methoden charakterisiert, insbesondere der Rastertunnelmikroskopie, Rastertunnelspektroskopie, Röntgen-Nahkanten-Absorptions-Spektroskopie und Photoelektronenspektroskopie, welche zudem durch theoretische Simulationen unter Verwendung der Dichtefunktionaltheorie ergänzt wurden. Tetra(p-hydroxyphenyl)porphyrin Moleküle ordnen sich durch Selbstorganisation zu verschiedenen, durch Wasserstoffbrückenbindungen stabilisierten Nanostrukturen an, welche in Abhängigkeit von dem Substratoberflächengitter untersucht wurden um das komplizierte Zusammenspiel von Molekül−Molekül und Molekül−Substrat-Wechselwirkungen bei der Selbstorganisation zu verstehen. Erhitzen der Adsorbatschichten dieses Moleküls führt zu einer schrittweisen Deprotonierung, und außerdem konnte auch ein Schalten der Leitfähigkeit einzelner Porphyrin-Moleküle durch lokale Deprotonierung mittels Spannungspulsen demonstriert werden. Eine Polymerisationsreaktion, welche auf der Ullmann-Reaktion basiert, aber direkt auf einer Oberfläche stattfindet, wurde für Kupfer-octabromotetraphenylporphyrin Moleküle, die auf Au(111) adsorbiert sind, gefunden. Nach einer thermischen Abspaltung der Bromatome von den Molekülen reagieren dabei die Radikalmoleküle bei hohen Temperaturen miteinander und bilden geordnete, kovalent gebundene Netzwerke aus. Die Bromabspaltung und die nachfolgenden Reaktionen und Veränderungen der elektronischen Struktur der Moleküle wurden ausführlich für die Substratoberflächen Au(111) sowie Ag(110) untersucht. Weiterhin, wird die Adsorption und Selbstorganisation von metall-freien Phthalocyanin-Molekülen auf einer Ag(110)-Oberfläche, und deren Selbstmetallierungsreaktion mit Silberatomen des Substrats umfassend und verständlich beschrieben. Zuletzt wurden organische Hybrid-Grenzflächen zwischen verschiedenen Metall-Phthalocyaninen untersucht, wobei ein Ladungstransfer zwischen Kobalt- und Platin-Phthalocyanin-Molekülen gefunden wurde. Dotierung gemischter Metall-Phthalocyanin-Filme durch Einlagerung von Kaliumatomen und deren selektive Adsorption im Molekülgitter führt zu einer deutlichen Veränderung der elektronischen Eigenschaften, aufgrund einer Ladungsübertragung an die Kobalt-Phthalocyanin Moleküle.:List of publications List of abbreviations 1 Introduction 2 Methods 2.1 Scanning tunneling microscopy 2.1.1 Theoretical description 2.1.2 STM imaging modes 2.1.3 Scanning tunneling spectroscopy 2.1.4 Technical aspect of the STM instrument 2.2 Low energy electron diffraction 2.3 Photoelectron spectroscopy 2.3.1 Principle 2.3.2 Theoretical description 2.3.3 Initial state effects 2.3.4 Final state effects 2.3.5 X-ray source 2.3.6 Technical aspects of PES 2.3.7 Resonant Photoelectron spectroscopy 2.4 Near-edge X-ray absorption fine structure spectroscopy 2.4.1 Principle 2.4.2 Polarization dependence 2.5 Density Functional Theory 2.5.1 Fundamental equations 2.5.2 Exchange-correlation functionals 2.5.3 Dispersion correction 2.5.4 Hubbard U correction 2.5.5 Basis set 2.5.6 Grid-based projector augmented wave (GPAW) method 2.6 Fundamentals of epitaxy and growth of molecular films 3 Experimental and computational details 3.1 Experimental setup 3.2 Sample preparation 3.3 Technical details for measurements 3.3.1 STM 3.3.2 PES 3.3.3 NEXAFS 3.4 Computational details 4 Metal-free tetra(p-hydroxylphenyl)porphyrin (H2THPP) 4.1 Interplay of hydrogen bonding and molecule-substrate interaction in self-assembled supra-molecular structures of H2THPP 4.1.1 Adlayer structures of H2THPP on Au(111) 4.1.2 Adlayer structures of H2THPP on Ag(111) 4.1.3 Adlayer structures of H2THPP on Ag(110) 4.1.4 Calculation of the adsorption energies and discussion 4.2 Manipulation of the electronic structure by local reversible dehydrogenation 4.2.1 STM and STS results 4.2.2 Discussion of the interconversion 4.2.3 Dosing of hydrogen gas on H2THPP 4.3 Photoelectron spectroscopy investigation of the temperature-induced deprotonation and substrate-mediated hydrogen transfer 4.3.1 Protonation and deprotonation at nitrogen atoms 4.3.2 Deprotonation at carbon atoms 4.3.3 Evolution of the valence band 4.4 Summary 5 Copper-octabromotetraphenylporphyrin (CuTPPBr8) 5.1 Introduction to surface-confined polymerization 5.2 Adsorption and polymerisation of CuTPPBr8 on Au(111) 5.2.1 XPS investigations 5.2.2 STM investigations of the molecular adlayer 5.2.3 DFT calculations 5.3 Adsorption and temperature-dependence of CuTPPBr8 on Ag(110) 5.3.1 XPS and NEXAFS investigations of CuTPPBr8 on Ag(110) 5.3.2 Adlayer structure and adsorption geometry of CuTPPBr8 on Ag(110) 5.4 Summary 6 Metal-free phthalocyanine (H2Pc) on Ag(110) 6.1 Adlayer structures of H2Pc on Ag(110) 6.2 Self-metalation of H2Pc on Ag(110) with silver surface atoms 6.2.1 Introduction to self-metalation 6.2.2 XPS investigations of the self-metalation 6.2.3 STM results of the self-metalation 6.2.4 DFT simulations of the metalation reaction path 6.3 Summary 7 Charge transfer in metallophthalocyanine blends and doping with potassium atoms 7.1 Charge transfer in platinum phthalocyanine – cobalt phthalocyanine dimers 7.1.1 XPS of PtPc−CoPc dimer layers 7.1.2 Resonant photoelectron spectroscopy of PtPc−CoPc dimer layers 7.2 Potassium doping of copper phthalocyanine − cobalt phthalocyanine mixed films 7.2.1 XPS of CuPc−CoPc mixed layers 7.2.2 UPS of CuPc−CoPc mixed layers 7.2.3 NEXAFS of CuPc−CoPc mixed layers 7.2.4 DFT calculations of the CuPc−CoPc dimer and K doping 7.3 Summary 8 Conclusion and outlook Bibliography Erklärung Lebenslauf Danksagung

Stepwise covalent synthesis of large molecules is often time consuming and laborious and thus generally ends in a low yield of the target product. It is also difficult to achieve a large desired product where the controlling force is a non-directional weak interaction. Instead, by utilizing stronger metal-ligand directional coordination bonding approach, one can easily prepare the desired large molecules using appropriate molecular units. Further attractive feature of this approach is the incorporation of functional groups into final structures to make the assemblies functional. It is found that symmetrical polypyridyl and rigid linkers have been used widely in the construction of finite supramolecules of Pd (II) and Pt(II). Flexible linkers are rarely used since they are less predictable in self-assembly and have a tendency to form undesired polymer. However, flexible linkers may generate pseudo rigid assemblies that can distort their shapes to obtain a more thermodynamically stable conformation for host-guest interactions. Similarly, use of non-symmetric or ambidentate linkers is not explored much. These linkers may generate a mixture of several linkage isomeric products and thus difficult to monitor the reaction. Moreover, isolation of these products in pure form is also a challenging task. On the other hand, recent research revealed that porous polyacetylene organic compounds are suitable sensors for the detection of electron deficient nitroaromatics, which are the chemical signatures of many commercial explosives. Possibility of discrete supramolecules as sensors for these explosives is very less studied. The main thrusts of the present investigation are to incorporate flexible and nonsymmetrical linkers in the construction of finite discrete assemblies of Pd/Pt; and to design appropriate π-electron rich supramolecules as sensors for the detection of electron deficient nitroaromatics. Chapter 1 of this thesis gives a brief introduction to the supramolecular chemistry. It also gives a brief introduction to the design principle of metal-ligand coordination driven selfassembly approach towards the generation of large architectures. Chapter 2 reports the synthesis of a series of two-dimensional supramolecular architectures via coordination driven self-assembly of Pt/Pd containing ditopic acceptors and non-symmetrical donor ligands. The use of non-symmetrical donor ligands in coordination driven self-assembly is a challenging task because they may generate a mixture of isomers due to different connectivity of the non-symmetric (ambidentate) linkers. But in all the cases exclusive formation of a single linkage isomer was established. Na-nicotinate was treated with [cis-(dppf)Pd(OTf)2] to yield [(dppf)3Pd3(L3)](CF3SO3)3(H2O)2(MeOH)7(Et2O) as the single linkage isomeric triangle. An analogous treatment using Na-isonicotinate instead of Na-nicotinate yielded a mixture of single isomeric square and triangle with the later one as the major product in solution. Further extension of this study using cis-(tmen)Pd(NO3)2 instead of [cis-(dppf)Pd(OTf)2] also showed the formation of a mixture of square and triangle [tmen = N,N,N’,N’- tetramethylethane-1,2-diamine]. Surprisingly, in both the cases square was the product which was crystallized exclusively in solid state though triangle was the major component in solution. The square-triangle equilibria in both the cases were studied by diffusion ordered NMR spectroscopy (DOSY) and variable temperature multinuclear NMR. Moreover, this chapter reports the incorporation of amide functionality into a Pt(II) nanoscopic molecular rectangle via self-assembly of an organometallic “clip” and a non-symmetric amide ligand. Chapter 3 presents synthesis of several metallamacrocycles via coordination driven selfassembly using Pd/Pt-P bonding interaction as driving force instead of much widely used Pd/Pt-N bonding interaction. It is also established that Pd/Pt-P bonding interaction is indeed better than the widely used Pd/Pt-N interaction. Several macrocycles were also synthesized by the combination of several Pd containing 90° angular subunits and a bisimidazole ditopic flexible donor. In this case also the bonding interaction between the imidazole and Pd(II) was found to be stronger than the interaction between pyridyl donor and Pd(II). Chapter 4 describes synthesis of several new Pt2 and Pt3 shape selective organometallic linkers incorporating ethynyl functionality. The Pt2 molecular clip was assembled with several linear dipyridyl linkers to prepare a series of molecular rectangles. In one case N, N’-bis(4-pyridylidene)ethylenediamine was used as donor to create a N4 pocket in the macrocycle. This rectangle was fluorescent in nature and showed efficient fluorescence quenching in solution upon binding of hard transition metal ions (Fe3+, Cu2+ and Ni2+) into the N4 pocket. The non-responsive nature of the fluorescence quenching upon addition of soft metal ions (Zn2+ and Cd2+) containing d10 configuration makes it an interesting example of sensor for transition metal ions. The Pt3 linkers were used in combination with organic clip-type linkers to prepare a series of molecular prisms by [2 + 3] self-assembly (Scheme 1). Incorporation of ethynyl functionality helped to make the resulting supramolecules π-electron rich and luminescent in nature. Possibility of these supramolecules as sensors for the detection of electron deficient nitroaromatics (TNT and picric acid), which are the chemical signatures of explosives has been explored. A complementary approach was also used to prepare trigonal prism using organic tritopic donor and the Pt2 molecular clip. Chapter 5 presents the design and self-assembly of two new flexible supramolecular nanoballs. These assemblies incorporate two flexible tritopic amide/ester based building blocks and were prepared in excellent yields (96-97%) via coordination driven selfassembly. The first one was resulted from the reaction of four equivalents of a new tritopic ester ligand N, N', N''-tris(4-pyridylmethyl) trimesic ester with three equivalents of C4 symmetric Pd(NO3)2. The second analogous structure was obtained by the selfassembly of the flexible N, N', N''-tris(3-pyridylmethyl)trimesic amide and Pd(NO3)2. The assemblies were characterized with multinuclear NMR spectroscopy, electrospray ionization mass spectroscopy, elemental analysis and TGA. The ester based ball showed the inclusion of NEt4 + in solution. This chapter also describes the exclusive formation of a Pt(II) trigonalbipyramidal (TBP) cage upon the treatment of a Pt(II) 90° acceptor with a new tripodal flexible ligand containing ester functionality. The formation of Pt(II) TBP cage in this case is due to the flexibility of the donor arms of the ligand due to the presence of flexible ester functional group. In continuation of this work, a rigid tripodal ligand 1,1,1-tris(4-pyridyl)COOR with an ester cap [where R = Ph-CH(C2H5)] was assembled with cis-(PEt3)2Pt(OTf)2 to yield a somewhat unusual double-square cage by [4 + 6] self-assembly.

Stepwise covalent synthesis of large molecules is often time consuming and laborious and thus generally ends in a low yield of the target product. It is also difficult to achieve a large desired product where the controlling force is a non-directional weak interaction. Instead, by utilizing stronger metal-ligand directional coordination bonding approach, one can easily prepare the desired large molecules using appropriate molecular units. Further attractive feature of this approach is the incorporation of functional groups into final structures to make the assemblies functional. It is found that symmetrical polypyridyl and rigid linkers have been used widely in the construction of finite supramolecules of Pd (II) and Pt(II). Flexible linkers are rarely used since they are less predictable in self-assembly and have a tendency to form undesired polymer. However, flexible linkers may generate pseudo rigid assemblies that can distort their shapes to obtain a more thermodynamically stable conformation for host-guest interactions. Similarly, use of non-symmetric or ambidentate linkers is not explored much. These linkers may generate a mixture of several linkage isomeric products and thus difficult to monitor the reaction. Moreover, isolation of these products in pure form is also a challenging task. On the other hand, recent research revealed that porous polyacetylene organic compounds are suitable sensors for the detection of electron deficient nitroaromatics, which are the chemical signatures of many commercial explosives. Possibility of discrete supramolecules as sensors for these explosives is very less studied. The main thrusts of the present investigation are to incorporate flexible and nonsymmetrical linkers in the construction of finite discrete assemblies of Pd/Pt; and to design appropriate π-electron rich supramolecules as sensors for the detection of electron deficient nitroaromatics. Chapter 1 of this thesis gives a brief introduction to the supramolecular chemistry. It also gives a brief introduction to the design principle of metal-ligand coordination driven selfassembly approach towards the generation of large architectures. Chapter 2 reports the synthesis of a series of two-dimensional supramolecular architectures via coordination driven self-assembly of Pt/Pd containing ditopic acceptors and non-symmetrical donor ligands. The use of non-symmetrical donor ligands in coordination driven self-assembly is a challenging task because they may generate a mixture of isomers due to different connectivity of the non-symmetric (ambidentate) linkers. But in all the cases exclusive formation of a single linkage isomer was established. Na-nicotinate was treated with [cis-(dppf)Pd(OTf)2] to yield [(dppf)3Pd3(L3)](CF3SO3)3(H2O)2(MeOH)7(Et2O) as the single linkage isomeric triangle. An analogous treatment using Na-isonicotinate instead of Na-nicotinate yielded a mixture of single isomeric square and triangle with the later one as the major product in solution. Further extension of this study using cis-(tmen)Pd(NO3)2 instead of [cis-(dppf)Pd(OTf)2] also showed the formation of a mixture of square and triangle [tmen = N,N,N’,N’- tetramethylethane-1,2-diamine]. Surprisingly, in both the cases square was the product which was crystallized exclusively in solid state though triangle was the major component in solution. The square-triangle equilibria in both the cases were studied by diffusion ordered NMR spectroscopy (DOSY) and variable temperature multinuclear NMR. Moreover, this chapter reports the incorporation of amide functionality into a Pt(II) nanoscopic molecular rectangle via self-assembly of an organometallic “clip” and a non-symmetric amide ligand. Chapter 3 presents synthesis of several metallamacrocycles via coordination driven selfassembly using Pd/Pt-P bonding interaction as driving force instead of much widely used Pd/Pt-N bonding interaction. It is also established that Pd/Pt-P bonding interaction is indeed better than the widely used Pd/Pt-N interaction. Several macrocycles were also synthesized by the combination of several Pd containing 90° angular subunits and a bisimidazole ditopic flexible donor. In this case also the bonding interaction between the imidazole and Pd(II) was found to be stronger than the interaction between pyridyl donor and Pd(II). Chapter 4 describes synthesis of several new Pt2 and Pt3 shape selective organometallic linkers incorporating ethynyl functionality. The Pt2 molecular clip was assembled with several linear dipyridyl linkers to prepare a series of molecular rectangles. In one case N, N’-bis(4-pyridylidene)ethylenediamine was used as donor to create a N4 pocket in the macrocycle. This rectangle was fluorescent in nature and showed efficient fluorescence quenching in solution upon binding of hard transition metal ions (Fe3+, Cu2+ and Ni2+) into the N4 pocket. The non-responsive nature of the fluorescence quenching upon addition of soft metal ions (Zn2+ and Cd2+) containing d10 configuration makes it an interesting example of sensor for transition metal ions. The Pt3 linkers were used in combination with organic clip-type linkers to prepare a series of molecular prisms by [2 + 3] self-assembly (Scheme 1). Incorporation of ethynyl functionality helped to make the resulting supramolecules π-electron rich and luminescent in nature. Possibility of these supramolecules as sensors for the detection of electron deficient nitroaromatics (TNT and picric acid), which are the chemical signatures of explosives has been explored. A complementary approach was also used to prepare trigonal prism using organic tritopic donor and the Pt2 molecular clip. Chapter 5 presents the design and self-assembly of two new flexible supramolecular nanoballs. These assemblies incorporate two flexible tritopic amide/ester based building blocks and were prepared in excellent yields (96-97%) via coordination driven selfassembly. The first one was resulted from the reaction of four equivalents of a new tritopic ester ligand N, N', N''-tris(4-pyridylmethyl) trimesic ester with three equivalents of C4 symmetric Pd(NO3)2. The second analogous structure was obtained by the selfassembly of the flexible N, N', N''-tris(3-pyridylmethyl)trimesic amide and Pd(NO3)2. The assemblies were characterized with multinuclear NMR spectroscopy, electrospray ionization mass spectroscopy, elemental analysis and TGA. The ester based ball showed the inclusion of NEt4 + in solution. This chapter also describes the exclusive formation of a Pt(II) trigonalbipyramidal (TBP) cage upon the treatment of a Pt(II) 90° acceptor with a new tripodal flexible ligand containing ester functionality. The formation of Pt(II) TBP cage in this case is due to the flexibility of the donor arms of the ligand due to the presence of flexible ester functional group. In continuation of this work, a rigid tripodal ligand 1,1,1-tris(4-pyridyl)COOR with an ester cap [where R = Ph-CH(C2H5)] was assembled with cis-(PEt3)2Pt(OTf)2 to yield a somewhat unusual double-square cage by [4 + 6] self-assembly.

Self–assembly has long been attracting chemists’ attention because it can yield fascinating supramolecular architectures in a single step. More precisely, metal–ligand coordination–driven self–assembly has stood out as an efficient methodology in this paradigm due to simple design principle and high predictability of the final molecular architectures. Moreover, one can envisage hierarchical nanoscopic molecular architectures with a vast range of size, shape and functionality via this methodology. Two–component self–assembly (involving one type of donor and one type of acceptor) is relatively easy to monitor and a widely used protocol. Whereas, multicomponent self–assembly (involving more than one types of donors/or acceptors) is too complex due to the possibility of formation of several products. The prime advantage of multicomponent self–assembly lies in one–pot construction of topologically complicated multifunctional architectures. Template– induced multicomponent self–assembly of discrete architectures is recently investigated to some extent. But, template–free multicomponent self–assembly of discrete architectures is rare in the literature. Physico–chemical property of a self–assembled product is coded in the functional groups present in its precursor building units. Functional supramolecular architectures have important applications in many potential fields such as chemosensing, drug delivery, supramolecular catalysis, etc. Porphyrin, pyrazole, imidazole, etc. functionalized organic molecules are hydrophilic as well as hydrophobic in nature. Introduction of such functionality in building units can lead to amphiphilic supramolecular complexes. Therefore, such complexes can be employed as hosts for versatile guests, or as molecular reactors for various chemical reactions. In general, counter ions block the cavity of ionic molecular architectures. Thus, when ionic molecular architectures are employed as hosts, they cannot fully provide their cavity towards guest molecules. In contrast, neutral molecular complexes are expected to be better hosts. It is well known that alkenyl/alkynyl heavy metal complexes exhibit efficient chemoluminescence due to facile metal to ligand charge transfer (MLCT). Hence, such complexes can be employed as efficient chemosensors towards the detection of electron deficient molecules such as nitroaromatics which are the chemical signatures of many powerful explosives. In these regards, a considerable effort is being paid recently to design and construct various functional supramolecular architectures. Symmetry and rigidity of building units increase predictability of the final product in self– assembly. In this regard, symmetric; rigid Pd(II)/Pt(II)–based acceptors and polypyridyl donors are explored extensively in metal–ligand coordination–driven self–assembly. In contrast to rigidity, flexibility endows building units to adopt thermodynamically most stable conformer/architecture. Hence, same set of building units can render different conformers/architectures in presence of different templates for the sake of suitable host–guest interactions. Contrary to high symmetry, asymmetry in building units leads to molecular architectures with polar environments. But, due to the possibility of formation of several isomeric products from the self–assembly involving such building units, it is difficult to monitor the reaction and purify the products. Hence, designing appropriate synthetic routes which can lead to formation of single isomeric products possessing flexible/asymmetric building units is a challenge to synthetic chemists. Investigations incorporated in the present thesis are focused to design and construct various 2D/3D discrete supramolecular architectures employing self–assembly of mainly Pd(II)/Pt(II) acceptors with N/O donors. Elemental analyses, IR/NMR/UV–Vis/fluorescence/mass spectroscopy and single crystal X–ray diffraction analysis are among prime techniques employed for characterization of the reported architectures. For a few cases, powder X–ray diffraction (PXRD) analysis and density functional theory (DFT) calculations are also carried out. CHAPTER 1 of the thesis provides a brief general introduction to self–assembly and supramolecular chemistry. It emphasizes on the metal–ligand coordination–driven self–assembly approach towards the construction of a library of 2D/3D supramolecular architectures. CHAPTER 2 describes formation of a series of template–induced and template–free discrete 3D Pd(II) molecular prisms via multicomponent self–assembly. Because of the possibility of formation of several products, multicomponent self–assembly is difficult to monitor. For example, several molecular architectures are expected from a three–component self–assembly involving a 90° acceptor [ca. cis–blocked Pd(II)], a 120° tritopic donor [ca. benzene–1,3,5– tricaboxylate (tma)] and a 180° donor [ca. 4,4'–bipyridine (4,4'–bpy) or pyrazine (pz)]. Interestingly, treatment of cis–(tmen)Pd(NO3)2 [tmen = N,N,N′,N′–tetramethylethylenediamine] with 4,4'–bpy and K3tma in 6 : 3 : 2 molar ratio at room temperature resulted in mainly a nanoscopic molecular trigonal prism [{(tmen)Pd}6(bpy)3(tma)2](NO3)6 (1) with three 4,4'–bpy pillars, two tma caps and six cis–(tmen)Pd connectors (Scheme 1). Scheme 1: Schematic representation of the formation of multicomponent self–assembled molecular trigonal prisms 1, 2 and 3. Surprisingly, the same reaction in presence of benzene–1,3,5–tricaboxylic acid (H3tma) as guest yielded exclusively the guest–encapsulated analogous molecular prism [{(tmen)Pd}6(bpy)3(tma)2(H3tma)2](NO3)6 (2; Scheme 1). It is also presented how variation of steric crowding at connectors (acceptors) influenced final outcomes. Self–assembly of cis– (en)Pd(NO3)2 [en = ethylenediamine] with 4,4'–bpy and K3tma in 6 : 3 : 2 molar ratio at room temperature resulted in a triply interlocked nanoscopic 3D coordination cage [{(en)Pd}6(bpy)3(tma)2]2(NO3)12 (3; Scheme 1). It is also shown that above trend is followed even upon changing the pillar length from 4,4'–bpy to pz. Aromatic –stacking interactions amog tma caps as well as among 4,4'–bpy pillars provided considerable stability to interlocked archirecture 3. Steric crowding due to the methyl groups in cis–(tmen)Pd connectors hindered intercalation and hence led to non–interlocked architecture 1. As expected, similar self–assembly using moderately crowded acceptor cis–(pn)Pd(NO3)2 [pn = 1,2–diaminopropane] with same donors 4,4'–bpy and K3tma resulted in a mixture of analogous triply interlocked and non– interlocked architectures in solution though it was found to be only triply interlocked architecture in solid state. Interestingly, irrespective of the steric crowding of the blocking amines, self– assembly in presence of H3tma as guest preferred exclusive formation of guest–encapsulated prisms of type 2 (Scheme 1). This is due to considerable stabilazation via aromatic –stacking interactions amog tma caps and H3tma guests. Formation of guest–free discrete molecular prisms (such as 1) and triply interlocked coordination cages (such as 3) were confirmed by spectroscopic and single crystal X–ray diffraction analyses. Whereas, formation of guest– encapsulated discrete molecular prisms (such as 2) was established by DOSY, ROESY 2D NMR spectroscpic study in conjunction with energy optimized geometry analysis. CHAPTER 3 reports design and syntheses of a series of porphyrin functionalized nanoscopic 3D molecular open prisms. Self–assembly of a C4 –symmetric tetratopic donor with a 90° ditopic acceptor can, in principle, lead to several architectures such as trigonal; tetragonal; pentagonal; hexagonal; etc. open prisms, closed cube or 1D oligomers. Both of 1,5,10,15–tetrakis(4– 12 pyridyl)porphyrin (L) and 1,5,10,15–tetrakis(3–pyridyl)porphyrin (L) possess pseudo C4 – 1 symmetry. Surprisingly, treatment of Lwith the 90° ditopic acceptor cis–(dppf)Pt(OTf)2 [dppf = diphenylphosphinoferrocene, OTf = trifluoromethanesulphonate] yielded exclusively an 1 unprecedented [6 + 12] self–assembled hexagonal open prism [(dppf)12Pt12L6](OTf)24 (4; Scheme 2). Scheme 2: Schematic representation of formation of [6 + 12] self–assembled molecular hexagonal open prism 4 and its Zn(II) embedded complex 4a. 2 In contrast, [3 + 6] self–assembled trigonal open prisms are adopted upon self–assembly of Lwith Pd(II)–based 90° ditopic acceptors. These complexes show facile incorporation of Zn(II) ions into porphyrin N4 –pockets. Moreover, they incorporate high microporosity in solid state and they are amphiphilic in nature due to porphyrin functionality. One of the trigonal open prisms revealed its considerably high adsorbate–adsorbent affinity towards non–polar gas such as N2 and protic solvent vapors such as water, methanol and ethanol. Formation of hexagonal and trigonal open prisms is fully authenticated by spectroscopic and single crystal X–ray diffraction analyses. CHAPTER 4 describes design and synthesis of a pyrazole functionalized flexible donor (L) and its self–assembly towards the construction of three nanoscopic 3D supramolecular discrete cages 5–7 (Scheme 3). Scheme 3: Schematic representation of formation of [4 + 6] self–assembled molecular double–square 5 and [2 + 3] self–assembled molecular trigonal bipyramids 6–7. 3 Due to flexibility, Lcan adopt different conformations and hence several isomeric architectures 3 are expected upon self–assembly. For example, self–assembly of Lwith a rigid ditopic 90° acceptor can lead to trigonal bipyramid (TBP), double–square, adamantanoid or truncated 3 tetrahedron. Treatment of Lwith cis–(tmen)Pd(NO3)2 yielded a [4 + 6] self–assembled double–3 square [(tmen)6Pd6L4](NO3)12 (5; Scheme 3). Much to our surprise, replacement of cis– (tmen)Pd(NO3)2 with CuCl2 or AgOTf yielded [2 + 3] self–assembled molecular TBP 33 [Cu3Cl6L2] (6) or [Ag3L2](OTf)3 (7), respectively (Scheme 3). CHAPTER 5 presents study of self–assembly involving flexible asymmetric donors and rigid 4 symmetric 90° acceptors. Three ambidentate donors 5–pyrimidinecarboxylate (L), nicotinate–56 N–oxide (L) and isonicotinate–N–oxide (L) were employed in self–assembly with symmetric rigid 90° acceptors cis–(dppf)M(OTf)2 [M = Pd(II)/Pt(II)]. Due to flexibility and different 464 connectivity of these donors L–L, several linkage isomers are expected. Treatment of Lwith cis–(dppf)M(OTf)2 in 1 : 1 molar ratio resulted in exclusive formation of single linkage isomeric 4 [3 + 3] self–assembled symmetric molecular triangles [(dppf)3M3L3](OTf)3 (8: M = Pd and 9: M = Pt), where the donors connected to metal centers in head–to–tailfashion (Scheme 4). Similar 56 reactions of Land Lwith cis–(dppf)M(OTf)2 resulted in self–sorting of [2 + 2] self–assembled molecular rhomboids 10–13 (Scheme 4). Exclusive self–selection of single linkage isomeric architectures 8, 9, 10 and 12 was fully established by spectroscopic as well as single crystal X– ray diffraction analyses. Though we could not obtain suitable X–ray diffraction quality single crystals of 11 and 13, exclusive formation of single isomeric [2 + 2] self–assembled rhomboids 131 was established by multinuclear NMR (H and P) in conjunction with ESI–MS spectroscopic studies. Scheme 4: Schematic representation of formation of complexes 8–13. Part A of the CHAPTER 6 describes how two neutral organometallic mononuclear chelates are formed upon treatment of disodium fumarate (,–unsaturated dicarboxylate) with cis– (dppf)Pd/Pt(OTf)2 at ambient conditions. Reaction of 90acceptors cis–(dppf)Pd/Pt(OTf)2 with fumarate is expected to result in [4 + 4] self–sorted molecular squares/or [2 + 2] self–sorted molecular rhomboids (Scheme 5). To our surprise, the above reactions led to an unusual reduction of C–C double bond followed by concomitant formation of mononuclear chelates [M(dppf)(C4H4O4)] (M = Pd for 14 and Pt for 15) via coordination with one of the carboxylate oxygen atoms and –carbon to metal centers (Scheme 5). Scheme 5: Schematic representation of formation of the complexes 14–15. Part B of the CHAPTER 6 describes design and synthesis of a novel shape selective “clip” 1 shaped bimetallic Pd(II) acceptor Mand its self–assembly with disodium fumarate to construct a neutral tetrametallic Pd(II) supramolecular rectangle 16 (Scheme 6, left). Similarly, a shape selective 180° bimetallic Pd(II) acceptor was also synthesized and employed in self–assembly with several “clip” shaped organic donors to achieve several cationic tetrametallic Pd(II) supramolecular rectangles. Scheme 6: Schematic representation of the formation of neutral Pd4 (left) and Pd2 (right) molecular rectangles. Moreover, synthesis of a neutral bimetallic Pd(II) molecular rectangle 17 via one–pot reaction of trans–(PEt3)2PdCl2 with 1,8–diethynylanthracene (Scheme 6, right) is also presented herein. These –electron rich rectangles exhibit prominent chemoluminescence. Chemosensitivity of these complexes towards the detection of electron deficient nitroaromatics via fluorescence study is also discussed in details in this section. (Pl refer the abstract file for figures).

Self–assembly has long been attracting chemists’ attention because it can yield fascinating supramolecular architectures in a single step. More precisely, metal–ligand coordination–driven self–assembly has stood out as an efficient methodology in this paradigm due to simple design principle and high predictability of the final molecular architectures. Moreover, one can envisage hierarchical nanoscopic molecular architectures with a vast range of size, shape and functionality via this methodology. Two–component self–assembly (involving one type of donor and one type of acceptor) is relatively easy to monitor and a widely used protocol. Whereas, multicomponent self–assembly (involving more than one types of donors/or acceptors) is too complex due to the possibility of formation of several products. The prime advantage of multicomponent self–assembly lies in one–pot construction of topologically complicated multifunctional architectures. Template– induced multicomponent self–assembly of discrete architectures is recently investigated to some extent. But, template–free multicomponent self–assembly of discrete architectures is rare in the literature. Physico–chemical property of a self–assembled product is coded in the functional groups present in its precursor building units. Functional supramolecular architectures have important applications in many potential fields such as chemosensing, drug delivery, supramolecular catalysis, etc. Porphyrin, pyrazole, imidazole, etc. functionalized organic molecules are hydrophilic as well as hydrophobic in nature. Introduction of such functionality in building units can lead to amphiphilic supramolecular complexes. Therefore, such complexes can be employed as hosts for versatile guests, or as molecular reactors for various chemical reactions. In general, counter ions block the cavity of ionic molecular architectures. Thus, when ionic molecular architectures are employed as hosts, they cannot fully provide their cavity towards guest molecules. In contrast, neutral molecular complexes are expected to be better hosts. It is well known that alkenyl/alkynyl heavy metal complexes exhibit efficient chemoluminescence due to facile metal to ligand charge transfer (MLCT). Hence, such complexes can be employed as efficient chemosensors towards the detection of electron deficient molecules such as nitroaromatics which are the chemical signatures of many powerful explosives. In these regards, a considerable effort is being paid recently to design and construct various functional supramolecular architectures. Symmetry and rigidity of building units increase predictability of the final product in self– assembly. In this regard, symmetric; rigid Pd(II)/Pt(II)–based acceptors and polypyridyl donors are explored extensively in metal–ligand coordination–driven self–assembly. In contrast to rigidity, flexibility endows building units to adopt thermodynamically most stable conformer/architecture. Hence, same set of building units can render different conformers/architectures in presence of different templates for the sake of suitable host–guest interactions. Contrary to high symmetry, asymmetry in building units leads to molecular architectures with polar environments. But, due to the possibility of formation of several isomeric products from the self–assembly involving such building units, it is difficult to monitor the reaction and purify the products. Hence, designing appropriate synthetic routes which can lead to formation of single isomeric products possessing flexible/asymmetric building units is a challenge to synthetic chemists. Investigations incorporated in the present thesis are focused to design and construct various 2D/3D discrete supramolecular architectures employing self–assembly of mainly Pd(II)/Pt(II) acceptors with N/O donors. Elemental analyses, IR/NMR/UV–Vis/fluorescence/mass spectroscopy and single crystal X–ray diffraction analysis are among prime techniques employed for characterization of the reported architectures. For a few cases, powder X–ray diffraction (PXRD) analysis and density functional theory (DFT) calculations are also carried out. CHAPTER 1 of the thesis provides a brief general introduction to self–assembly and supramolecular chemistry. It emphasizes on the metal–ligand coordination–driven self–assembly approach towards the construction of a library of 2D/3D supramolecular architectures. CHAPTER 2 describes formation of a series of template–induced and template–free discrete 3D Pd(II) molecular prisms via multicomponent self–assembly. Because of the possibility of formation of several products, multicomponent self–assembly is difficult to monitor. For example, several molecular architectures are expected from a three–component self–assembly involving a 90° acceptor [ca. cis–blocked Pd(II)], a 120° tritopic donor [ca. benzene–1,3,5– tricaboxylate (tma)] and a 180° donor [ca. 4,4'–bipyridine (4,4'–bpy) or pyrazine (pz)]. Interestingly, treatment of cis–(tmen)Pd(NO3)2 [tmen = N,N,N′,N′–tetramethylethylenediamine] with 4,4'–bpy and K3tma in 6 : 3 : 2 molar ratio at room temperature resulted in mainly a nanoscopic molecular trigonal prism [{(tmen)Pd}6(bpy)3(tma)2](NO3)6 (1) with three 4,4'–bpy pillars, two tma caps and six cis–(tmen)Pd connectors (Scheme 1). Scheme 1: Schematic representation of the formation of multicomponent self–assembled molecular trigonal prisms 1, 2 and 3. Surprisingly, the same reaction in presence of benzene–1,3,5–tricaboxylic acid (H3tma) as guest yielded exclusively the guest–encapsulated analogous molecular prism [{(tmen)Pd}6(bpy)3(tma)2(H3tma)2](NO3)6 (2; Scheme 1). It is also presented how variation of steric crowding at connectors (acceptors) influenced final outcomes. Self–assembly of cis– (en)Pd(NO3)2 [en = ethylenediamine] with 4,4'–bpy and K3tma in 6 : 3 : 2 molar ratio at room temperature resulted in a triply interlocked nanoscopic 3D coordination cage [{(en)Pd}6(bpy)3(tma)2]2(NO3)12 (3; Scheme 1). It is also shown that above trend is followed even upon changing the pillar length from 4,4'–bpy to pz. Aromatic –stacking interactions amog tma caps as well as among 4,4'–bpy pillars provided considerable stability to interlocked archirecture 3. Steric crowding due to the methyl groups in cis–(tmen)Pd connectors hindered intercalation and hence led to non–interlocked architecture 1. As expected, similar self–assembly using moderately crowded acceptor cis–(pn)Pd(NO3)2 [pn = 1,2–diaminopropane] with same donors 4,4'–bpy and K3tma resulted in a mixture of analogous triply interlocked and non– interlocked architectures in solution though it was found to be only triply interlocked architecture in solid state. Interestingly, irrespective of the steric crowding of the blocking amines, self– assembly in presence of H3tma as guest preferred exclusive formation of guest–encapsulated prisms of type 2 (Scheme 1). This is due to considerable stabilazation via aromatic –stacking interactions amog tma caps and H3tma guests. Formation of guest–free discrete molecular prisms (such as 1) and triply interlocked coordination cages (such as 3) were confirmed by spectroscopic and single crystal X–ray diffraction analyses. Whereas, formation of guest– encapsulated discrete molecular prisms (such as 2) was established by DOSY, ROESY 2D NMR spectroscpic study in conjunction with energy optimized geometry analysis. CHAPTER 3 reports design and syntheses of a series of porphyrin functionalized nanoscopic 3D molecular open prisms. Self–assembly of a C4 –symmetric tetratopic donor with a 90° ditopic acceptor can, in principle, lead to several architectures such as trigonal; tetragonal; pentagonal; hexagonal; etc. open prisms, closed cube or 1D oligomers. Both of 1,5,10,15–tetrakis(4– 12 pyridyl)porphyrin (L) and 1,5,10,15–tetrakis(3–pyridyl)porphyrin (L) possess pseudo C4 – 1 symmetry. Surprisingly, treatment of Lwith the 90° ditopic acceptor cis–(dppf)Pt(OTf)2 [dppf = diphenylphosphinoferrocene, OTf = trifluoromethanesulphonate] yielded exclusively an 1 unprecedented [6 + 12] self–assembled hexagonal open prism [(dppf)12Pt12L6](OTf)24 (4; Scheme 2). Scheme 2: Schematic representation of formation of [6 + 12] self–assembled molecular hexagonal open prism 4 and its Zn(II) embedded complex 4a. 2 In contrast, [3 + 6] self–assembled trigonal open prisms are adopted upon self–assembly of Lwith Pd(II)–based 90° ditopic acceptors. These complexes show facile incorporation of Zn(II) ions into porphyrin N4 –pockets. Moreover, they incorporate high microporosity in solid state and they are amphiphilic in nature due to porphyrin functionality. One of the trigonal open prisms revealed its considerably high adsorbate–adsorbent affinity towards non–polar gas such as N2 and protic solvent vapors such as water, methanol and ethanol. Formation of hexagonal and trigonal open prisms is fully authenticated by spectroscopic and single crystal X–ray diffraction analyses. CHAPTER 4 describes design and synthesis of a pyrazole functionalized flexible donor (L) and its self–assembly towards the construction of three nanoscopic 3D supramolecular discrete cages 5–7 (Scheme 3). Scheme 3: Schematic representation of formation of [4 + 6] self–assembled molecular double–square 5 and [2 + 3] self–assembled molecular trigonal bipyramids 6–7. 3 Due to flexibility, Lcan adopt different conformations and hence several isomeric architectures 3 are expected upon self–assembly. For example, self–assembly of Lwith a rigid ditopic 90° acceptor can lead to trigonal bipyramid (TBP), double–square, adamantanoid or truncated 3 tetrahedron. Treatment of Lwith cis–(tmen)Pd(NO3)2 yielded a [4 + 6] self–assembled double–3 square [(tmen)6Pd6L4](NO3)12 (5; Scheme 3). Much to our surprise, replacement of cis– (tmen)Pd(NO3)2 with CuCl2 or AgOTf yielded [2 + 3] self–assembled molecular TBP 33 [Cu3Cl6L2] (6) or [Ag3L2](OTf)3 (7), respectively (Scheme 3). CHAPTER 5 presents study of self–assembly involving flexible asymmetric donors and rigid 4 symmetric 90° acceptors. Three ambidentate donors 5–pyrimidinecarboxylate (L), nicotinate–56 N–oxide (L) and isonicotinate–N–oxide (L) were employed in self–assembly with symmetric rigid 90° acceptors cis–(dppf)M(OTf)2 [M = Pd(II)/Pt(II)]. Due to flexibility and different 464 connectivity of these donors L–L, several linkage isomers are expected. Treatment of Lwith cis–(dppf)M(OTf)2 in 1 : 1 molar ratio resulted in exclusive formation of single linkage isomeric 4 [3 + 3] self–assembled symmetric molecular triangles [(dppf)3M3L3](OTf)3 (8: M = Pd and 9: M = Pt), where the donors connected to metal centers in head–to–tailfashion (Scheme 4). Similar 56 reactions of Land Lwith cis–(dppf)M(OTf)2 resulted in self–sorting of [2 + 2] self–assembled molecular rhomboids 10–13 (Scheme 4). Exclusive self–selection of single linkage isomeric architectures 8, 9, 10 and 12 was fully established by spectroscopic as well as single crystal X– ray diffraction analyses. Though we could not obtain suitable X–ray diffraction quality single crystals of 11 and 13, exclusive formation of single isomeric [2 + 2] self–assembled rhomboids 131 was established by multinuclear NMR (H and P) in conjunction with ESI–MS spectroscopic studies. Scheme 4: Schematic representation of formation of complexes 8–13. Part A of the CHAPTER 6 describes how two neutral organometallic mononuclear chelates are formed upon treatment of disodium fumarate (,–unsaturated dicarboxylate) with cis– (dppf)Pd/Pt(OTf)2 at ambient conditions. Reaction of 90acceptors cis–(dppf)Pd/Pt(OTf)2 with fumarate is expected to result in [4 + 4] self–sorted molecular squares/or [2 + 2] self–sorted molecular rhomboids (Scheme 5). To our surprise, the above reactions led to an unusual reduction of C–C double bond followed by concomitant formation of mononuclear chelates [M(dppf)(C4H4O4)] (M = Pd for 14 and Pt for 15) via coordination with one of the carboxylate oxygen atoms and –carbon to metal centers (Scheme 5). Scheme 5: Schematic representation of formation of the complexes 14–15. Part B of the CHAPTER 6 describes design and synthesis of a novel shape selective “clip” 1 shaped bimetallic Pd(II) acceptor Mand its self–assembly with disodium fumarate to construct a neutral tetrametallic Pd(II) supramolecular rectangle 16 (Scheme 6, left). Similarly, a shape selective 180° bimetallic Pd(II) acceptor was also synthesized and employed in self–assembly with several “clip” shaped organic donors to achieve several cationic tetrametallic Pd(II) supramolecular rectangles. Scheme 6: Schematic representation of the formation of neutral Pd4 (left) and Pd2 (right) molecular rectangles. Moreover, synthesis of a neutral bimetallic Pd(II) molecular rectangle 17 via one–pot reaction of trans–(PEt3)2PdCl2 with 1,8–diethynylanthracene (Scheme 6, right) is also presented herein. These –electron rich rectangles exhibit prominent chemoluminescence. Chemosensitivity of these complexes towards the detection of electron deficient nitroaromatics via fluorescence study is also discussed in details in this section. (Pl refer the abstract file for figures).

Thesis (Ph. D.)--University of Chicago, Department of Chemistry, August 2003.
CD-ROM reproduces the entire dissertation in PDF format. Includes bibliographical references. Also available on the Internet.

博士
國立臺北科技大學
工程科技研究所
95
In recent years, the design, self-assembly, and application of supramolecular coordination polymers have been extensively studied. The organic ligands with different geometry shape and angle have been designed and synthesized. The reactions of these organic ligands with the metallic ions form the corresponding functional coordination polymers. In this dissertation, the metallic ions were chosen from Co+2, Ni+2, Cu+2, Zn+2 and Cd+2. Two types of the organic ligands were selected for self-assembly. One type of ligand was based on literature synthesized, the other type of ligand was designed and synthesized. We synthesized five new pyrazine-modulated ligands, [(N-Pyrazin-2-yl)(N''-pyridin-2-yl)pyridine-2,6-diamine (H2pzpypy), N,N''-bis(pyridin- 2-yl)pyrazine-2,6-diamine (H2pypypz), (N-Pyrazin-2-yl)-(N''-pyridin-2-yl)pyrazine- 2,6-diamine (H2pzpypz), N,N''–bis(pyrazin-2-yl)-pyridine-2,6-diamine (H2pzpzpy) and N,N''–bis(pyrazin-2-yl)pyrazine-2,6-diamine (H2pzpzpz). By coordinating with metal ions Cu+2 and Ni+2, several 1-D, 2-D and 3-D supramolecular coordination polymers determined by X-ray single crystal diffraction have been obtained. Another new ligand, trans-4,4''-azo-1,2,4-triazole (atr) was also synthesized for the construction of coordination polymers. The ligand is a planar molecule with two triazoles linked by an azo group. It could be served as a multi-dentate ligand or a good linkage ligand. A series of Co(II) polymeric compounds with 1-D, 2-D and 3-D frameworks have been successfully synthesized and characterized structurally. The ligand, 1,4-bis(3-pyridyl)-2,3-diaza-1,3-butadiene (3-bpd), has also been used for the synthesis of three novel coordination polymers. Two novel coordination polymers have the same chemical composition, [ZnCl2(3-bpd)]n and they show different structural conformations with one forming a helical chain and the other a square-wave chain. The intermolecular C−H•••Cl hydrogen bonds in both structures play important roles in the formation of 3-D framework. The coordination polymer [Ni2(NO3)4(3-bpd)3]n•nEtOH, with all the bridging ligands in a bis-monodentate mode connecting to the Ni(II) ions, formed a 3-D metal-organic polymeric framework that shows a 1-D microporous channel with dimensions of ca. 6.7 x 8.5 Å2 along the a-axis. The EtOH guest molecules are intercalated into these channels. The reaction of N,N''-bis(4-pyridylmethyl)oxalamide (4py-ox) with Co+2 and Cd+2 formed two novel supramolecular coordination compounds, [CoCl2(4py-ox)]n•0.5nH2O, and [Cd(NO3)2(4py-ox)1.5]n, respectively. The structure of [CoCl2(4py-ox)]n•0.5nH2O features a 1-D zigzag chain. Two interwoven chains create a cavity of ca 8.6 x 8.6 Å2, which produces a 3-D channel and water molecules are held in the channel by hydrogen bonds. The structure of [Cd(NO3)2(4py-ox)1.5]n shows a 2-D sheet polymeric framework and the neighboring sheets are interlaced, and the 3-D structure of this compound is microporous.

This thesis describes work towards the development of a range of supramolecular devices and materials based on cyclodextrin host-guest interactions, and/or short peptide structures. The first such device targeted was a photoswitchable molecular lariat composed of a [c2] (cyclic, two-component) asymmetric daisy chain. Upon combining the two hetero monomer units it was found that a [c2]-dimer was not formed. The next phase of research involved the design of a second type of supramolecular device, also based on cyclodextrin host-guest inclusion complexes, this time serving to produce a change in peptide secondary structure. A range of devices were synthesised giving several modifications; increasing the stability of hexavaline beta sheets, reducing the PPII (polyproline type II) helicity in pentaalanine and introducing beta sheet character to pentaalanine. Furthermore, an azobenzene moiety was introduced as a photo-switchable cyclodextrin guest, enabling PPII helicity to be switched between states of increased and decreased structure via photoirraditation. This principle was then developed to give a device which not only produced a change in peptide structure but also brought about a change in function, in this case metal-binding ability. Upon cyclodextrin host-guest [c2]-dimer formation, beta sheet structure was induced in a short peptide strand which facilitated the arrangement of histidine residues in order to bind to a metal ion in a pseudo-chelating arrangement. The unmodified peptide, with no cyclodextrin or guest attached did not bind to zinc ions, whereas the cyclodextrin dimer was found to bind to Zn2+ with a Ka of 2,223 M-1. The system was then investigated in the solid-phase and a crystal was grown wherein [c1]-complexes were bound to Zn2+ in tetrameric assemblies. In addition, the same crystal structure was observed in the absence of Zn2+ showing that the system pre-assembles to form a crystal lattice with vacant metal binding sites. A number of smaller studies were also performed to explore the possibility of the application of peptide chemistry techniques and principles to supramolecular concepts. The solid-phase synthesis technique used to make peptide sequences was investigated as a method for the preparation of rotaxanes. Despite several attempts no interlocked structures were synthesised, however a method was established for the mobilisation of a cyclodextrin onto a stationary phase. -Sheet peptide-peptide interactions, in conjunction with cyclodextrin host-guest interactions were then explored as a method for the generation of self-assembling polymers. A range of polymeric structures were considered, however within all the systems examined it was found that none formed. Finally, it was observed that a peptide amphiphile (PA), synthesized during the preparation of a metal-binding cyclodextrin dimer, formed a gel in acetonitrile/water mixtures, DMF and acetone at just 0.06 wt.%. The compound did not form a gel in water, despite its structural similarity to previously reported PAs, but did obey the structure-property relationships determined for these hydrogels. This suggests that despite the difference in solvents, assembly of these organo and hydrogels is the same and indicates a new strategy for the modification of PAs in order to gel target solvents.

Over the past few decades, supramolecular self-assembly has become an alternative synthetic tool for constructing targeted discrete molecular architectures. Among various interactions, metal-ligand coordination has attracted great attention owing to high bond enthalpy (15−50 Kcal/mol) and predictable directionality. The basic principle of metal-ligand directed self-assembly relies on the proper designing of information encoded rigid complementary building units (a transition metal based acceptor and a multidentate organic donor) that self-recognize themselves in a chemically reasonable way (depends on their bite angle and symmetry) during self-assembly process. As far as acceptor units are concerned, Pd(II) and Pt(II) metal-based cis-blocked 90° acceptors have so far been used greatly for the construction of a library of 2D/3D discrete supramolecular architectures due to their rigid square planar geometry and kinetic lability. However, in some cases the efforts to design finite supramolecular architectures using a cis-blocked 90° acceptor in combination with a bulky donor ligand were unsuccessful, which may be due to the steric demands of donor ligand. Moreover, the resulted assemblies from such cis-blocked 90° building unit are mostly non-fluorescent in nature and limit the possibility of using them as chemosensors for various practical applications. Unlike that of rigid square-planar Pt(II) and Pd(II)-metal based building blocks, the use of other transition metal-based building units for the construction of discrete nanoscopic molecular architectures are known to lesser extent, mainly because of their versatile coordination geometries. However, some of the half-sandwiched piano-stool complexes of late transition metals like Ru, Os, Ir and Rh are known to maintain the stable octahedral geometry under various reaction conditions. Moreover, the self-assembly using redox active transition metal-based building units may lead to redox active assemblies. On the other hand, symmetrical rigid donors have been widely used as the favorite choices for the purpose of constructing desired product mainly due to their predictable directionality. Flexible linkers are not predictable in their directionality during self-assembly process and thus results mostly in undesired polymeric products. Furthermore, metal-ligand directed self-assembly provides opportunity to introduce multifunctionality in a single step within/onto the final supramolecular architectures. Among various functional groups, the incorporation of unsaturated ethynyl functionality is expected to enrich the final assemblies to be π-electron-rich and the attachment of ethynyl functionality with heavy transition metal ions are known to be luminescent in nature due to the facile metal to ligand charge transfer (MLCT). Hence, the final supramolecular complexes can be used as potential fluorescence sensors for electron-deficient nitroaromatics, which are the chemical signature of most of the commercially available explosives. The main thrust of the present investigation is focused on the judicious design and syntheses of multifaceted 2D/3D supramolecular architectures of finite shapes, sizes and functionality using Pt(II)/Ru(II) based “shape-selective” organometallic building blocks and investigation of their application as chemosensors. CHAPTER 1 of the thesis presents a general review on the core concepts of self-assembly and supramolecular chemistry. In particular, it underlines the importance of metal-ligand directional bonding approach for designing a vast plethora of discrete 2D/3D supramolecular architectures with tremendous variation in topology. CHAPTER 2 describes the design and syntheses of a series of 2D metallamacrocycles using carbazole-functionalized shape-selective 90° building units. A new Pt2II organometallic 90° acceptor 3,6-bis[trans-Pt(PEt3)2(NO3)(ethynyl)]carbazole (M1) containing ethynyl functionality is synthesized via Sonagashira coupling reaction and characterized. The combination of M1 with three different flexible ditopic donors (L1−L3) afforded [2 + 2] self-assembled molecular squares (1−3), respectively [where L1 = 1,3-bis(4-pyridyl)isophthalamide; L2 = 1,3-bis(3-pyridyl)isophthalamide; L3 = 1,2-bis(4-pyridyl)ethane] (Scheme 1). Scheme 1: Schematic presentation of the formation of a series of [2 + 2] self-assembled molecular squares. An equimolar (1:1) combination of same acceptor M1 with rigid linear ditopic donors (L4-L5) yielded [4 + 4] self-assembled octanuclear molecular squares 4 and 5, respectively [L4 = 4,4’-bipyridine; L5 = trans-1,2-bis(4-pyridyl)ethylene]. Conversely, a similar reaction of M1 with an amide-based unsymmetrical linear flexible ditopic donor L6 resulted in the formation a [2 + 2] self-sorted molecular rhomboid (6a) as a single product [L6 = N-(4-pyridyl)isonicotinamide]. Despite the possibility of several linkage isomeric macrocycles (rhomboids, triangles and squares) due to different connectivity of the ambidentate linker, the formation of a single and symmetrical molecular rhomboid 6a as an exclusive product is an interesting observation. This chapter also presents the synthesis and characterization of a complementary 90° dipyridyl donor 3,6-bis(4-pyridylethynyl)carbazole (L7). Stoichiometric combination of L7 with several PdII/PtII-based 90° acceptors (M2−M4) yielded [2 + 2] self-assembled molecular “bowl” shaped macrocycles (7−9) respectively, in good yields [M2 = cis-(dppf)Pd(CF3SO3)2; M3 = cis-(dppf)Pt(CF3SO3)2; M4 = cis-(tmen)Pd(NO3)2]. All these newly synthesized macrocycles were characterized by various spectroscopic techniques and molecular structures of some of them were confirmed by single crystal X-ray diffraction analysis. In addition to their syntheses and characterization, fluorescence chemosensing ability for various analytes was investigated. Macrocycle 1 is a system composed of amide-based receptor units and carbazole-based fluorophore moieties. The fluorescence study of 1 elicited a dramatic enhancement in the fluorescence intensity upon gradual addition of P2O74- anion in DMF/H2O solvent mixture, whereas similar titration under identical condition with other anions like F-, ClO4-, and H2PO4- did not show such change. Hence, molecular square 1 can be used as selective fluorescence sensor for pyrophosphate (P2O74-) anion. Due to their extended π-conjugation, macrocycles 3-4 were used as fluorescence sensors for electron-deficient nitroaromatics, which are the chemical signatures of many commercially available explosives. The fluorescence study showed a marked quenching of initial fluorescence intensity of the macrocycles(3-4) upon gradual addition of picric acid (PA) and they exhibited large fluorescence quenching responses with high selectivity for nitroaromatics among various other electron deficient aromatic compounds tested. As macrocycle 7 has large concave aromatic surface, it was utilized as a suitable host for large convex guest such as fullerene C60. The fluorescence quenching titration study suggested that macrocycle 7 forms a stable ~1:1 host-guest complex with C60 and the calculated association constant (KSV) is 1.0 × 105 M-1. CHAPTER 3 presents two-component coordination-driven self-assembly of a series of [2 + 2] molecular rectangles and a [2 + 4] self-assembled molecular tetragonal prism. An equimolar combination of pre-designed linear PtII2-acceptors M5−M6 separately with three different “clip” donors (L2, L8−L9) led to the formation of [2 + 2] self-assembled tetranuclear cationic molecular rectangles (10−15), respectively [M5 = 1,4-bis[trans-Pt(PEt3)2(NO3)(ethynyl)] benzene; M6 = 4,4’-bis[trans-Pt(PEt3)2(CF3SO3)(ethynyl)]biphenyl; L8 = 1,3-bis(3-pyridyl)ethynylbenzene; L9 = 1,8-bis(4-pyridyl)ethynylanthracene]. Rectangles 10-15 showed strong fluorescence in solution owing to their extended π-conjugation. Amide-functionalized rectangle 10 was used as a macrocyclic receptor for dicarboxylic acids. Solution state fluorescence study showed that rectangle 10 selectively binds (KSV = 1.4 × 104 M-1) with maleic acid by subsequent enhancement in emission intensity and addition of other analogous aliphatic dicarboxylic acids such as fumaric, succinic, adipic, mesaconic and itaconic acids causes no change in the emission spectra; thereby demonstrated its potential use as macrocyclic receptor in sensor applications. Since rectangle 15 is enriched with π-conjugation, it was examined as a fluorescence sensor for electron-deficient nitroaromatics such as picric acid, which is often considered as a secondary chemical explosive. The fluorescence study of 15 showed a significant quenching of initial emission intensity upon titrating with picric acid (PA) and it exhibited the largest fluorescence quenching response with high selectivity for picric acid. Scheme 2: Schematic representation of formation of [2 + 4] self-assembled of molecular tetragonal prism. This chapter also describes two-component coordination [2 + 4] self-assembly of a pyrene-based PtII8 tetragonal prism (16) as shown in Scheme 2, using a newly designed tetratopic organometallic acceptor (M7; 1,3,6,8-tetrakis[trans-Pt(PEt3)2(NO3)(ethynyl)]pyrene) in combination with an amide-based “clip” donor (L2) and propensity of this prism (16) as a selective fluorescence sensor for nitroaromatic explosives has been examined both in solution as well as in thin-film. CHAPTER 4 reports the synthesis and structural characterization of a series of Ru(II)-based bi-and tetra-nuclear metallamacrocycles and hexanuclear trigonal prismatic cages. In principle, the self-assembly of a “clip” acceptor with an asymmetrical ditopic donor is expected to give two different linkage isomeric (head-to-tail and head-to-head) molecular rectangles because of different bond connectivity of the donor. However, the equimolar combination of half-sandwiched p-cymene binuclear Ru(II)-based “clip” acceptors (M8−M9) and an amide-based ambidentate donor (L6) resulted in the self-sorting of single linkage (head-to-tail) isomeric rectangles 17−18 as only products, respectively [M8 = [Ru2(μ-η4-C2O4)(MeOH)2(η 6-p-cymene)2](CF3SO3)2; M9 = [Ru2(μ- η4-C6H2O4)(MeOH)2(η 6-p-cymene)2](CF3SO3)2]. Molecular structures of these head-to-tail linkage isomeric rectangles were unambiguously proved by single crystal X-ray diffraction analysis. Likewise, the self-assembly of oxalato-bridged Ru(II) acceptor M8 with a rigid dipyridyl “clip” donor L8 yielded a tetranuclear cationic pincer complex 19, while a similar reaction of M8 with an anthracene-functionalized “clip” donor L9 having shorter distance (between their reactive sites) compared to L8 led to the formation of [1 + 1] self-assembled macrocycle 20. This chapter also represents the design and synthesis of two hexanuclear trigonal prismatic cages (21−22) from the self-assembly of a π-electron rich tripyridyl donor (L10; 1,3,5-tris(4-pyridylethynyl)benzene) in combination with binuclear acceptors M8 and M9, respectively (Scheme 3). Formation of these prismatic cages was initially characterized using various spectroscopic techniques and the molecular structure of oxalato-bridged prism 21 was confirmed by single crystal X-ray diffraction analysis. In addition to the structural characterization, the pincer complex 19 and trigonal prismatic cages 21−22 were used as fluorescence sensors for nitroaromatic explosives owing to their large internal porosity and their π-electron rich nature. Scheme 3: Schematic representation of the formation of [3 + 2] self-assembled trigonal prismatic cage. CHAPTER 5 covers the syntheses of a few discrete metallamacrocycles using flexible imidazole/carboxylate based donors instead of much widely employed polypyridyl donors. The metal-ligand directed self-assembly of oxalato-bridged acceptor M8 and an imidazole-based tetratopic donor (L11; 1,2,4,5-tetrakis(imidazol-1-yl)benzene) in methanol afforded [2 + 1] self-assembled tetranuclear macrocycle 23. Conversely, the similar combination of L11 with 2,5-dihydroxy-1,4-benzoquinonato-bridged binuclear complex (M9) in 1:2 molar ratio in methanol resulted in an octanuclear cage 24. Both the complexes (23−24) were isolated as their triflate salts in high yields and were characterized by various spectroscopic methods including single crystal X-ray diffraction analysis. Scheme 4: Schematic representation of formation of an octanuclear incomplete Ru(II) open prism via ruthenium-oxygen coordination driven self-assembly. This chapter also explains the self-sorting of an unusual octanuclear incomplete prism [Ru8(η6-p-cymene)8(tma)2(μ-η4-C2O4)2(OMe)4](CF3SO3)2 (25) via ruthenium-oxygen coordination driven self-assembly of building block M8 and sodium benzene-1,3,5-tricarboxylate (L12) (Scheme 4). Electronic absorption study indicated that prism 25 exhibited a remarkable shape-selective binding affinity for 1,3,5-trihydroxybenzene (phluoroglucinol) via multiple hydrogen bonding interactions and such shape-selective binding was confirmed by single crystal X-ray diffraction analysis. (For figures pl see the abstract file)

Over the past few decades, supramolecular self-assembly has become an alternative synthetic tool for constructing targeted discrete molecular architectures. Among various interactions, metal-ligand coordination has attracted great attention owing to high bond enthalpy (15−50 Kcal/mol) and predictable directionality. The basic principle of metal-ligand directed self-assembly relies on the proper designing of information encoded rigid complementary building units (a transition metal based acceptor and a multidentate organic donor) that self-recognize themselves in a chemically reasonable way (depends on their bite angle and symmetry) during self-assembly process. As far as acceptor units are concerned, Pd(II) and Pt(II) metal-based cis-blocked 90° acceptors have so far been used greatly for the construction of a library of 2D/3D discrete supramolecular architectures due to their rigid square planar geometry and kinetic lability. However, in some cases the efforts to design finite supramolecular architectures using a cis-blocked 90° acceptor in combination with a bulky donor ligand were unsuccessful, which may be due to the steric demands of donor ligand. Moreover, the resulted assemblies from such cis-blocked 90° building unit are mostly non-fluorescent in nature and limit the possibility of using them as chemosensors for various practical applications. Unlike that of rigid square-planar Pt(II) and Pd(II)-metal based building blocks, the use of other transition metal-based building units for the construction of discrete nanoscopic molecular architectures are known to lesser extent, mainly because of their versatile coordination geometries. However, some of the half-sandwiched piano-stool complexes of late transition metals like Ru, Os, Ir and Rh are known to maintain the stable octahedral geometry under various reaction conditions. Moreover, the self-assembly using redox active transition metal-based building units may lead to redox active assemblies. On the other hand, symmetrical rigid donors have been widely used as the favorite choices for the purpose of constructing desired product mainly due to their predictable directionality. Flexible linkers are not predictable in their directionality during self-assembly process and thus results mostly in undesired polymeric products. Furthermore, metal-ligand directed self-assembly provides opportunity to introduce multifunctionality in a single step within/onto the final supramolecular architectures. Among various functional groups, the incorporation of unsaturated ethynyl functionality is expected to enrich the final assemblies to be π-electron-rich and the attachment of ethynyl functionality with heavy transition metal ions are known to be luminescent in nature due to the facile metal to ligand charge transfer (MLCT). Hence, the final supramolecular complexes can be used as potential fluorescence sensors for electron-deficient nitroaromatics, which are the chemical signature of most of the commercially available explosives. The main thrust of the present investigation is focused on the judicious design and syntheses of multifaceted 2D/3D supramolecular architectures of finite shapes, sizes and functionality using Pt(II)/Ru(II) based “shape-selective” organometallic building blocks and investigation of their application as chemosensors. CHAPTER 1 of the thesis presents a general review on the core concepts of self-assembly and supramolecular chemistry. In particular, it underlines the importance of metal-ligand directional bonding approach for designing a vast plethora of discrete 2D/3D supramolecular architectures with tremendous variation in topology. CHAPTER 2 describes the design and syntheses of a series of 2D metallamacrocycles using carbazole-functionalized shape-selective 90° building units. A new Pt2II organometallic 90° acceptor 3,6-bis[trans-Pt(PEt3)2(NO3)(ethynyl)]carbazole (M1) containing ethynyl functionality is synthesized via Sonagashira coupling reaction and characterized. The combination of M1 with three different flexible ditopic donors (L1−L3) afforded [2 + 2] self-assembled molecular squares (1−3), respectively [where L1 = 1,3-bis(4-pyridyl)isophthalamide; L2 = 1,3-bis(3-pyridyl)isophthalamide; L3 = 1,2-bis(4-pyridyl)ethane] (Scheme 1). Scheme 1: Schematic presentation of the formation of a series of [2 + 2] self-assembled molecular squares. An equimolar (1:1) combination of same acceptor M1 with rigid linear ditopic donors (L4-L5) yielded [4 + 4] self-assembled octanuclear molecular squares 4 and 5, respectively [L4 = 4,4’-bipyridine; L5 = trans-1,2-bis(4-pyridyl)ethylene]. Conversely, a similar reaction of M1 with an amide-based unsymmetrical linear flexible ditopic donor L6 resulted in the formation a [2 + 2] self-sorted molecular rhomboid (6a) as a single product [L6 = N-(4-pyridyl)isonicotinamide]. Despite the possibility of several linkage isomeric macrocycles (rhomboids, triangles and squares) due to different connectivity of the ambidentate linker, the formation of a single and symmetrical molecular rhomboid 6a as an exclusive product is an interesting observation. This chapter also presents the synthesis and characterization of a complementary 90° dipyridyl donor 3,6-bis(4-pyridylethynyl)carbazole (L7). Stoichiometric combination of L7 with several PdII/PtII-based 90° acceptors (M2−M4) yielded [2 + 2] self-assembled molecular “bowl” shaped macrocycles (7−9) respectively, in good yields [M2 = cis-(dppf)Pd(CF3SO3)2; M3 = cis-(dppf)Pt(CF3SO3)2; M4 = cis-(tmen)Pd(NO3)2]. All these newly synthesized macrocycles were characterized by various spectroscopic techniques and molecular structures of some of them were confirmed by single crystal X-ray diffraction analysis. In addition to their syntheses and characterization, fluorescence chemosensing ability for various analytes was investigated. Macrocycle 1 is a system composed of amide-based receptor units and carbazole-based fluorophore moieties. The fluorescence study of 1 elicited a dramatic enhancement in the fluorescence intensity upon gradual addition of P2O74- anion in DMF/H2O solvent mixture, whereas similar titration under identical condition with other anions like F-, ClO4-, and H2PO4- did not show such change. Hence, molecular square 1 can be used as selective fluorescence sensor for pyrophosphate (P2O74-) anion. Due to their extended π-conjugation, macrocycles 3-4 were used as fluorescence sensors for electron-deficient nitroaromatics, which are the chemical signatures of many commercially available explosives. The fluorescence study showed a marked quenching of initial fluorescence intensity of the macrocycles(3-4) upon gradual addition of picric acid (PA) and they exhibited large fluorescence quenching responses with high selectivity for nitroaromatics among various other electron deficient aromatic compounds tested. As macrocycle 7 has large concave aromatic surface, it was utilized as a suitable host for large convex guest such as fullerene C60. The fluorescence quenching titration study suggested that macrocycle 7 forms a stable ~1:1 host-guest complex with C60 and the calculated association constant (KSV) is 1.0 × 105 M-1. CHAPTER 3 presents two-component coordination-driven self-assembly of a series of [2 + 2] molecular rectangles and a [2 + 4] self-assembled molecular tetragonal prism. An equimolar combination of pre-designed linear PtII2-acceptors M5−M6 separately with three different “clip” donors (L2, L8−L9) led to the formation of [2 + 2] self-assembled tetranuclear cationic molecular rectangles (10−15), respectively [M5 = 1,4-bis[trans-Pt(PEt3)2(NO3)(ethynyl)] benzene; M6 = 4,4’-bis[trans-Pt(PEt3)2(CF3SO3)(ethynyl)]biphenyl; L8 = 1,3-bis(3-pyridyl)ethynylbenzene; L9 = 1,8-bis(4-pyridyl)ethynylanthracene]. Rectangles 10-15 showed strong fluorescence in solution owing to their extended π-conjugation. Amide-functionalized rectangle 10 was used as a macrocyclic receptor for dicarboxylic acids. Solution state fluorescence study showed that rectangle 10 selectively binds (KSV = 1.4 × 104 M-1) with maleic acid by subsequent enhancement in emission intensity and addition of other analogous aliphatic dicarboxylic acids such as fumaric, succinic, adipic, mesaconic and itaconic acids causes no change in the emission spectra; thereby demonstrated its potential use as macrocyclic receptor in sensor applications. Since rectangle 15 is enriched with π-conjugation, it was examined as a fluorescence sensor for electron-deficient nitroaromatics such as picric acid, which is often considered as a secondary chemical explosive. The fluorescence study of 15 showed a significant quenching of initial emission intensity upon titrating with picric acid (PA) and it exhibited the largest fluorescence quenching response with high selectivity for picric acid. Scheme 2: Schematic representation of formation of [2 + 4] self-assembled of molecular tetragonal prism. This chapter also describes two-component coordination [2 + 4] self-assembly of a pyrene-based PtII8 tetragonal prism (16) as shown in Scheme 2, using a newly designed tetratopic organometallic acceptor (M7; 1,3,6,8-tetrakis[trans-Pt(PEt3)2(NO3)(ethynyl)]pyrene) in combination with an amide-based “clip” donor (L2) and propensity of this prism (16) as a selective fluorescence sensor for nitroaromatic explosives has been examined both in solution as well as in thin-film. CHAPTER 4 reports the synthesis and structural characterization of a series of Ru(II)-based bi-and tetra-nuclear metallamacrocycles and hexanuclear trigonal prismatic cages. In principle, the self-assembly of a “clip” acceptor with an asymmetrical ditopic donor is expected to give two different linkage isomeric (head-to-tail and head-to-head) molecular rectangles because of different bond connectivity of the donor. However, the equimolar combination of half-sandwiched p-cymene binuclear Ru(II)-based “clip” acceptors (M8−M9) and an amide-based ambidentate donor (L6) resulted in the self-sorting of single linkage (head-to-tail) isomeric rectangles 17−18 as only products, respectively [M8 = [Ru2(μ-η4-C2O4)(MeOH)2(η 6-p-cymene)2](CF3SO3)2; M9 = [Ru2(μ- η4-C6H2O4)(MeOH)2(η 6-p-cymene)2](CF3SO3)2]. Molecular structures of these head-to-tail linkage isomeric rectangles were unambiguously proved by single crystal X-ray diffraction analysis. Likewise, the self-assembly of oxalato-bridged Ru(II) acceptor M8 with a rigid dipyridyl “clip” donor L8 yielded a tetranuclear cationic pincer complex 19, while a similar reaction of M8 with an anthracene-functionalized “clip” donor L9 having shorter distance (between their reactive sites) compared to L8 led to the formation of [1 + 1] self-assembled macrocycle 20. This chapter also represents the design and synthesis of two hexanuclear trigonal prismatic cages (21−22) from the self-assembly of a π-electron rich tripyridyl donor (L10; 1,3,5-tris(4-pyridylethynyl)benzene) in combination with binuclear acceptors M8 and M9, respectively (Scheme 3). Formation of these prismatic cages was initially characterized using various spectroscopic techniques and the molecular structure of oxalato-bridged prism 21 was confirmed by single crystal X-ray diffraction analysis. In addition to the structural characterization, the pincer complex 19 and trigonal prismatic cages 21−22 were used as fluorescence sensors for nitroaromatic explosives owing to their large internal porosity and their π-electron rich nature. Scheme 3: Schematic representation of the formation of [3 + 2] self-assembled trigonal prismatic cage. CHAPTER 5 covers the syntheses of a few discrete metallamacrocycles using flexible imidazole/carboxylate based donors instead of much widely employed polypyridyl donors. The metal-ligand directed self-assembly of oxalato-bridged acceptor M8 and an imidazole-based tetratopic donor (L11; 1,2,4,5-tetrakis(imidazol-1-yl)benzene) in methanol afforded [2 + 1] self-assembled tetranuclear macrocycle 23. Conversely, the similar combination of L11 with 2,5-dihydroxy-1,4-benzoquinonato-bridged binuclear complex (M9) in 1:2 molar ratio in methanol resulted in an octanuclear cage 24. Both the complexes (23−24) were isolated as their triflate salts in high yields and were characterized by various spectroscopic methods including single crystal X-ray diffraction analysis. Scheme 4: Schematic representation of formation of an octanuclear incomplete Ru(II) open prism via ruthenium-oxygen coordination driven self-assembly. This chapter also explains the self-sorting of an unusual octanuclear incomplete prism [Ru8(η6-p-cymene)8(tma)2(μ-η4-C2O4)2(OMe)4](CF3SO3)2 (25) via ruthenium-oxygen coordination driven self-assembly of building block M8 and sodium benzene-1,3,5-tricarboxylate (L12) (Scheme 4). Electronic absorption study indicated that prism 25 exhibited a remarkable shape-selective binding affinity for 1,3,5-trihydroxybenzene (phluoroglucinol) via multiple hydrogen bonding interactions and such shape-selective binding was confirmed by single crystal X-ray diffraction analysis. (For figures pl see the abstract file)