A major function assessed by Nature is the transport of a cargo between two different media, such as anions through cell membranes. Mimicking this function using complex systems is one of the biggest challenge of supramolecular chemistry. Metallo-organic cages are an important breakthrough in the encapsulation and transport of small molecules, providing a crucial platform for the development of systems chemistry. Binding a network member within a tetrahedral cage allows it to be hidden and then revealed upon receipt of a release signal, or transported as a cargo between spatially distant parts of a network. Larger capsules may also isolate subsystems from each other in the manner of vesicles. These dynamic architectures are synthesised by self-assembly, which involves the simultaneous formation of multiple coordinative and dynamic covalent linkages during the same overall synthetic process. Their shape and binding properties can be tuned by changing the subcomponents such as metals or ligands. Great progress has been reported in recent years in the development of three-dimensional cages that can interact with specific guest species, but there are limitations associated with the transport of these systems. Recent work by Nitschke et al. have successfully addressed practical separations problems by transporting a tetrahedral cage and its cargo from water into an ionic liquid layer. However, this system is not ideal as the process is triggered by an anion exchange not by a direct stimulus. This thesis reports the synthesis of an ionic liquid inspired tetrahedral system achieving reversible transport between water and an immiscible organic solvent driven by a change in temperature. Once the switchable capsules were obtained and characterised, their ability to move between different solvent phases upon heating was investigated. A capsule-mediated transport system as developed that is both directional and reversible. The flow of the capsule and its encapsulated cargo is directed using stimuli such as temperature modification. Ultimately an apparatus that allows the switchable capsules to move along a channel has been developed.

Biological systems construct varieties of self-assembled architectures with incredible elegance and precession utilizing proteins as subunits to accomplish widespread functions. Inspired by natural systems, construction of artificial model systems with such sophistication and delicacy has become an intriguing field of research over the last two decades using so-called self-assembly process. Judiciously selected complementary building units encoded with specific chemical and structural information can be self-assembled into pre-programmed abiological architectures in a manner similar to biological self-assembly. In this regard, kinetically labile metal-ligand coordination has become an efficient and powerful protocol for the construction of highly intricate structures with specific topology and functionality due to its simple design principle, high bond enthalpy, and predictable directionality. Two-component self-assembly is very widely used methodology and easy to monitor. Recently, multi-component self-assembly has come up as an alternative and effective pathway to achieve complex architectures connecting more than two components in a single step. However, formation of selective single product from multicomponents is entropically unfavorable. Only a very few 3D architectures have been known, that are obtained from a mixture of ditopic and tri- or tetratopic donors with metal acceptors with or without employing templates. Development of template-free multicomponent architectures is still in its infancy. Strong tendency of Pd(II)/Pt(II) to attain square-planar geometry around the metal center and kinetically labile nature of Pd(II)/Pd(II)-N(pyridine) bonds made them chemists’ favourite to engineer desired supramolecular coordination architectures with structural resemblance to Platonic or Archimedean solids by employing symmetrical pyridyl donors due to their predictable directionality. In case of poly-imidazole donors, free rotation of C-N bond connecting imidazole and phenyl ring allows various dispositions of the donating nitrogen with respect to the aromatic backbone, and therefore, the structural topology of the architectures, made of poly-imidazole ligands becomes much more interesting as compared to symmetrical Platonic or Archimedean solids. The physico-chemical properties of self-assembled coordination cages depend on the structures of the complexes. Presence of large internal cavity surrounded by aromatic core, provides an excellent environment for the encapsulation of varieties of guest molecule or as nano-reactors for different organic transformations. Structural investigation in terms of packing interactions, solvent molecules, intermolecular channels can sometimes determine the property of such self-assembled materials as well. Presence of acidic water as well as H-bonded 3D-networks of water molecules in molecular pockets make them potential material for proton conduction. In addition, metal-ligand coordination offers opportunity to introduce new functionality through pre-synthetic modification of the building constituents to influence the property of the supramolecular systems. Incorporation of unsaturated ethynyl functionality attached to the heavy transition metal is expected to exhibit efficient luminescence due to the facile metal to ligand charge transfer (MLCT). Hence, the final assemblies can be employed as chemosensors for electron-deficient nitroaromatics, which are the chemical signature of many of the commercially available explosives. The present investigation is focused on design and construction of discrete, nanoscopic coordination cages with unusual structural topology employing mainly imidazole-based donors with Pd(II)/Pt(II) acceptors and their applications in catalysis, chemosensing, and proton conduction. CHAPTER 1 of the thesis provides a general introduction to self-assembly focusing on the importance and advantages of metal-ligand directional bonding approach towards the construction of supramolecular architectures with various structural topologies. This chapter also includes a brief review on the applications of such coordination cages in various fields especially as ‘molecular flask’ for the observation of unique chemical phenomena and unusual reactions. Part A of CHAPTER 2 describes the synthesis of a new hollow Pd6 water soluble cage [{(tmen)Pd}6(timb)4](NO3)12 (1) via two-component self-assembly of a triimidazole donor and 90° Pd(II) acceptor [tmen = N,N,N’,N’-tetramethylethylenediamine, timb = 1,3,5-tris(1-imidazolyl)benzene]. The assembly was successfully crystallized with a hydrophilic dianionic benzoquinone derivative (formed in situ by the decomposition of DDQ) as [{(tmen)Pd}6(timb)4](NO3)10()2(H2O)18 (3), and a hydrophobic sterically demanding aromatic aldehyde as [{(tmen)Pd}6(timb)4](NO3)12{()4a}2(H2O)27 (5a) [where 2H2 = 2,3-dichloro-5,6-dihydroxycyclohexa-2,5diene-1,4-dione, 4a = 1-pyrenecarboxaldehyde,  = exohedral and  = endohedral] to confirm the hydrophobic nature of the cavity. Experiments were carried out to show that the hydrophobic confined nanospace of the cage (1) catalyses the Knoevenagel condensation of a series of different aromatic monoaldehydes with active methylene compounds in ‘green’ aqueous medium. The Knoevenagel condensation reaction is basically a dehydration reaction because water is a by-product. So the presence of water should, in principle, promote the backward reaction as per Le Chatelier’s principle. In general, these reactions with organic substrates are not performed in water. However, difficulty has been overcome using hydrophobic cavity of the cage. It has also been established that the cavity of the cage also enhances the rate of Diels-Alder reaction of 9-hydroxymethylanthracene with N-phenylmaleimide/N-cyclohexylmaleimide. Figure 1. Catalytic Knoevenagel condensation and Diels-Alder reaction using hydrophobic cavity of the cage (1) in aqueous medium. Part B of CHAPTER 2 reports unique three-component self-assembly incorporating both tri- and tetra-topic donors. Until now, a very few 3D-architectures have been known that are obtained from self-assembly of ditopic and tri- or tetratopic donors with metal acceptors. Scheme 1. Three-component self-assembly of a Pd7 cage (1) from cis-blocked Pd(II) 90° acceptor (M), tri-imidazole (timb) and tetra-imidazole (tim) donors. Self-assembled multicomponent discrete architecture composed of both tri- and tetra-topic donors is yet to be reported due to difficulty in prediction of the final structure from the mixture of ligands having multiple donor sites. The first example of self-sorted Pd7 molecular boat [{(tmen)Pd}7(timb)2(tim)2](NO3)14(H2O)20 (1) [tmen = N,N,N’,N’-tetramethylethylenediamine, timb = 1,3,5-tris(1-imidazolyl)-benzene, tim = 1,2,4,5-tetrakis(1-imidazolyl)benzene] was synthesized via three-component self-assembly of cis-(tmen)Pd(NO3)2, tetra- (tim) and tri-topic donors (timb) in a 7:2:2 ratio. The cavity of this cage was also utilized as a nanoreactor for catalytic Knoevenagel condensations of a series of aromatic aldehydes with 1,3-dimethylbarbituric acid (e) and Meldrum’s acid (f) in aqueous media. CHAPTER 3 presents the results of an investigation on how simple variation of length and coordination mode of linear donors can self-discriminate into markedly different complex architectures, from Pd8 molecular swing [{(tmen)Pd}8(tim)2(bpy)4](NO3)16 (1) or [{(tmen)Pd}8(tim)2(stt)5](NO3)6 (2) to Pd6 molecular boat [{(tmen)Pd}6(tim)2(bpe/dpe/pin/dpb)2](NO3)12, (3/4/5/6). Also by enhancing denticity [bidentate to tridentate (ptp)] as well as introducing asymmetry, they self-sort into Pd7 molecular tent [{(tmen)Pd}7(tim)2(ptp)2](NO3)14 (7) by employing it in a self-assembly of cis-(tmen)Pd(NO3)2 and tetraimidazole (tim) donor [where tmen = N,N,N’,N’-tetramethylethylenediamine, bpy = 4,4’-bipyridyl, stt = sodium terephthalate, bpe = trans-1,2-bis(4-pyridyl)ethylene, dpe = 1,2-di(pyridin-4-yl)ethane, pin = N-(pyridin-4-yl)isonicotinamide, dpb = 1,4-di(pyridin-4-yl)benzene, ptp = 6'-(pyridin-4-yl)-3,4':2',4''-terpyridine, and tim = 1,2,4,5-tetrakis(1- imidazolyl)benzene]. In these cases, control of the geometrical principles and stereo-electronic preferences of the building units allowed the formation of such intricate architectures. Some of these assemblies represent first examples of such types of structures, and their formation would not be anticipated by taking into account only the geometry of the donor and acceptor building units. In addition to their direct structural confirmation using single crystal X-ray diffraction analysis, propensity of the assemblies (1 and 3) to form inclusion complexes with large guest like C60 in solution was also demonstrated by fluorescence quenching experiment. The high KSV values for both the assemblies 1 (1.0 × 10-5 M-1) and 2 (1.6 × 10-6 M-1) with C60 indicated the propensity of these assemblies to form complexes with C60 in solution. Furthermore, inspection of crystal packing of other five complexes (2 and 4 - 7) revealed the presence of water molecules H-bonded with NO3– (O-H···O=N) and 3D H-bonded networks of water in the intermolecular pockets. Interestingly, the present complexes (2 and 4 - 7) show high conductivity across low-humidity range at ambient temperature and achieve a conductivity of ~10-3 Scm-1 at 75% relative humidity and 296 K. These supra-molecular architectures represent a new generation of discrete materials that display high proton conductivity under ambient conditions with activation energy comparable to that of Nafion. Scheme 2. Exclusive formation of Pd8 molecular swings (1 and 2), Pd6 molecular boats (3-6), and Pd7 molecular tent (7) via self-sorting. CHAPTER 4 presents self-selection by synergistic effect of morphological information and coordination ability of the ligands through specific coordination interactional algorithms within dynamic supramolecular systems involving a tetratopic Pd(II) acceptor and three different pyridine- and imidazole-based donors (La - Lc) [La = 1,3-bis((E)-2-(pyridin-3-yl)vinyl)benzene, Lb = 1,3-di(1H-imidazol-1-yl)benzene, and Lc = tris(4-(1H-imidazol-1-yl)phenyl)amine]. Three different cages, ‘paddle wheel’ cluster Pd2(La)4(NO3)4 (2a), molecular barrel Pd3(Lb)6(NO3)6 (2b) and molecular sphere Pd6(Lc)8(NO3)12 (2c) were first synthesized via two-component self-assembly of a tetratopic Pd(II) acceptor (1) and individual pyridine- and imidazole-based donors (La - Lc). When all the four components were allowed to interact in a complex reaction mixture, only one out of three cages was isolated. The inherent dynamic nature of the kinetically labile coordination bond allows constitutional adaptation through component exchange in the competition experiment involving multiple constituents to self-organize into specific combination and thereby, achieve the thermodynamically most stable assembly. The preferential binding affinity towards a particular partner was also established by transforming a non-preferred cage to a preferred cage by the interaction with the appropriate ligand and thus, this represents the first examples of two-step cage-to-cage transformation through constitutional evolution of Figure 2. Cage-to-cage transformation from non-preferred cage to preferred cage upon treatment with appropriate ligand; and Nyquist plots of the complexes (2b and 2c) under 98% RH condition and ambient temparature. dynamic systems induced by both coordination ability and geometry of the ligand. Moreover, computational study further supported the fact that coordination interaction of imidazole moiety to Pd(II) is enthalpically more preferred compared to pyridine which drives the selection process. In addition, analysis of crystal packing of both the complexes (2b and 2c) indicated the presence of strong H-bonds between NO3- and water molecules; as well as H-bonded 3D-networks of water. Interestingly, both the complexes exhibit promising proton conductivity (10-5 to ca. 10-3 S cm-1) at ambient temperature under relative humidity of ~98% with low activation energy. CHAPTER 5 covers design and synthesis of new organometallic building block 1,3,5-tris(4-trans-Pt(PEt3)2I(ethynyl)phenyl)benzene (1) incorporating Pt-ethynyl functionality and [2 + 3] self-assembly of its nitrate analogue 1,3,5-tris(4-trans-Pt(PEt3)2(ONO2)(ethynyl)phenyl)benzene (2) with “clip” type bidentate donors (L1 – L3) separately afforded three trigonal prismatic architectures (3a – 3c), respectively (Scheme 3), Scheme 3. Schematic presentation of three different donors (L1 – L3) and a new planar tritopic acceptor (2) and their [3 + 2] self-assembly into trigonal prismatic architectures (3a - 3c). [L1 = N1,N3-di(pyridin-3-yl)isophthalamide; L2 = 1,3-bis((E)-2-(pyridin-3-yl)vinyl)benzene; L3 = 1,3-bis(pyridin-3-ylethynyl)benzene]. All these prisms were characterized and their shapes/sizes are predicted through geometry optimization employing molecular mechanics universal force field (MMUFF) simulation. The extended -conjugation including the presence of Pt-ethynyl functionality make them electron rich as well as luminescent in nature. As expected, cages 3b and 3c exhibit fluorescent quenching in solution upon addition of picric acid [PA], which is a common constituent of many explosives. Interestingly, the non-responsive nature of fluorescent intensity towards other electron-deficient nitro-aromatic explosives (NAEs) makes them promising selective sensors for PA with a detection limit deep down to ppb. Complexes 3b – c represent the first examples of molecular metallocages as selective sensors for picric acid. Furthermore, solid-state quenching of fluorescent intensity of the thin film of 3b upon exposure to saturated vapor of picric acid draws special attention for infield application.

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Ce travail traite de la synthèse et de la caractérisation de nouvelles cages moléculaires discrètes riches en électrons préparées via la méthodologie d'auto-assemblage dirigée par les métaux, ainsi que de leurs propriétés redox et d’encapsulation. Les concepts généraux guidant la méthodologie d’auto-assemblage pilotée par les métaux sont présentés. Trois types de ligands tétratopiques rédox-actifs (L) constitués de tétrathiafulvalène (TTF), de dithiol-fluorène (DTF) ou de tétrathiafulvalène π étendu (exTTF) ont été conçus. Leur capacité à générer des cages auto-assemblées avec divers complexes (M) a été étudiée. Dans le premier cas, des métallacages M8L2 dont la géométrie offre une opportunité unique de favoriser des interactions inter-TTF étroites au cours du processus d’oxydation ont été décrites. Ces interactions ont été confirmées par des études électrochimiques ainsi que par DRX à partir d’un sel oxydé électrocristallisé. Dans le second cas, plusieurs auto-assemblages discrets MxLy (cages, clips) ont été obtenus à partir de nouveaux ligands électroactifs basés sur l'unité 9- (1,3-dithiol-2-ylidène) fluorène (DTF). Leurs propriétés rédox ainsi que leur capacité à complexer des unités électro-déficientes sont fortement dépendantes de la géométrie de l’auto-assemblage. Concernant le ligand exTTF, de grandes métallacages électroactives M12L6 (environ 4 000 Å3) ont été obtenus par combinaison avec des complexes trans de palladium ou d'argent. Ces dernières se désassemblent lors de l'oxydation, donnant lieu à une transformation sans précédent d'une cage métallique discrète en un polymère de coordination. Enfin, un nouveau squelette aromatique benzo[1,2-b:4,5-b'] dithiophène est décrit en tant qu’alternative aux dérivés riches en électrons π étendus. Le rôle critique des interactions non-covalentes 1,5 S ···S est démontré par une approche combinée expérimentale et théorique. / This work deals with the synthesis and characterization of new electron-rich discrete molecular cages, prepared via the coordination-driven self-assembly methodology, as well as on evaluating their redox and host-guest properties. The general concepts guiding the metal-driven self-assembly methodology are presented. Three types of redox-active tetratopic ligands (L) featuring either a tetrathiafulvalene (TTF), a dithiol-fluorene (DTF) or a π-extended tetrathiafulvalene (exTTF) have been designed. Their ability to generate self-assembled cages upon combination with various metal complexes (M) has been studied. In the first case, M8L2 metallacages were obtained, whose geometry offers a unique opportunity to promote close inter-TTF interactions upon oxidation, as confirmed through electrochemical studies as well as from single-crystal DRX from an electrocrystallized oxidized salt. In the second case, several discrete self-assemblies MxLy (cages, clips) were obtained and characterized from new electro-active ligands based on the 9-(1,3-dithiol-2-ylidene)fluorene (DTF) unit. Their redox properties as well as their binding ability towards electro-deficient planar species show a strong dependence to the self-assembly geometry. Considering the exTTF ligand, large (ca. 4000 Å3) electroactive M12L6 metallacages were obtained from combining with trans palladium or silver complexes. Le latter exhibits a disassembling process upon oxidation, giving rise to an unprecedented redox-triggered transformation of discrete metalla-cage into a coordination polymer. Finally, a new benzo[1,2-b:4,5-b'] dithiophene aromatic scaffold is investigated as an alternative π-extended electron-rich derivative. The critical role of non-covalent 1,5 S···S interactions is demonstrated by a combined experimental and theoretical approach.

The first chapter of this thesis introduces the fundamental concepts governing the design and synthesis of supramolecular complexes. By illustrating the synthesis of several coordination cages reported in the literature, the principles underlying the construction of coordination cages by subcomponent self-assembly are elucidated. Ionic liquids are then proposed as solvents for cage systems; general methods for the preparation and synthesis of these solvents are described. The second chapter explores the use of ionic liquids as solvents for existing coordination cages. Potential methods of characterising these cages in ionic liquids are discussed; cages are demonstrated to be stable and capable of encapsulating guests in these ionic environments; and systems in which cages have good solubility in ionic liquids are designed. Building upon these observations, a triphasic sorting system is presented such that each of three different host-guest complexes are soluble in only one of three immiscible liquid phases. In contrast to the static triphasic system described in the second chapter, the third chapter explores directed phase transfer of coordination cages and their cargos from water, across a phase interface, and into an ionic liquid phase. The host-guest complex can then be recycled from the ionic liquid layer back into water after several additional steps. Furthermore, phase transfer of cationic cages is used to separate a mixture of cationic and anionic host-guest complexes. In the fourth chapter, fully reversible phase transfer of coordination cages is developed. Using anion exchange to modulate the solubility of three different cationic cages, reversible transport between water and ethyl acetate is demonstrated. Sequential phase transfer can also be achieved such that, from a mixture of cubic (+16) and tetrahedral (+8) cages, the cubic cage transfers from water to ethyl acetate before the tetrahedral cage. This process is fully reversible; upon the addition of a hydrophilic anion, the tetrahedral cage returns from ethyl acetate to water before the cubic cage.

Deep learning methods applied to chemistry can speed the discovery of novel compounds and facilitate the design of highly complex structures that are both valid and have important societal applications. Here, we present a pioneering exploration into the use of Generative Artificial Intelligence (GenAI) to design coordination cages within the field of supramolecular chemistry. Specifically, the study leverages GraphINVENT, a graph-based deep generative model, to facilitate the automated generation of tetrahedral coordination cages. Through a combination of computational tools and cheminformatics, the research aims to extend the capabilities of GenAI, traditionally applied in simpler chemical contexts, to the complex and nuanced arena of coordination cages. The approach involves a variety of training strategies, including initial pre-training on a large dataset (GDB-13) followed by transfer learning targeted at generating specific coordination cage structures. Data augmentation techniques were also applied to enrich training but did not yield successful outcomes. Several other strategies were employed, including focusing on single metal ion structures to enhance model familiarity with Fe-based cages and extending training datasets with diverse molecular examples from the ChEMBL database. Despite these strategies, the models struggled to capture the complex interactions required for successful cage generation, indicating potential limitations with both the diversity of the training datasets and the model’s architectural capacity to handle the intricate chemistry of coordination cages. However, training on the organic ligands (linkers) yielded successful results, emphasizing the benefits of focusing on smaller building blocks. The lessons learned from this project are substantial. Firstly, the knowledge acquired about generative models and the complex world of supramolecular chemistry has provided a unique opportunity to understand the challenges and possibilities of applying GenAI to such a complicated field. The results obtained in this project have highlighted the need for further refinement of data handling and model training techniques, paving the way for more advanced applications in the future. Finally, this project has not only raised our understanding of the capabilities and limitations of GenAI in coordination cages, but also set a foundation for future research that could eventually lead to breakthroughs in designing novel cage structures. Further study could concentrate on learning from the linkers in future data-driven cage design projects. / Deep learning-metoder (djup lärande metoder) som tillämpas på kemi kan påskynda upptäckten av nya molekyler och underlätta utformningen av mycket komplexa strukturer som både är giltiga och har viktiga samhällstillämpningar. Här presenterar vi en banbrytande undersökning av användningen av generativ artificiell intelligens (GenAI) för att designa koordinationsburar inom supramolekylär kemi. Specifikt utnyttjar studien GraphINVENT, en grafbaserad djup generativ modell, för att underlätta den automatiska genereringen av tetraedriska koordinationsburar. Genom en kombination av beräkningsverktyg och kemiinformatik syftar forskningen till att utöka kapaciteten hos GenAI, som traditionellt tillämpas i enklare kemiska sammanhang, till den komplexa och nyanserade arenan för koordinationsburar. Metoden innebar inledande förträning på ett brett dataset (GDB-13) följt av transferinlärning inriktad på att generera specifika koordinationsburstrukturer. Dataförstärkningstekniker användes också för att berika träningen men gav inte några lyckade resultat. Flera strategier användes, inklusive fokusering på enstaka metalljonsystem för att förbättra modellens förtrogenhet med Fe-baserade burar och utöka träningsdataset med olika molekylära exempel från ChEMBL-databasen. Trots dessa strategier hade modellerna svårt att fånga de komplexa interaktioner som krävs för framgångsrik generering av burar, vilket indikerar potentiella begränsningar inom både mångfalden av träningsdataset och modellens arkitektoniska kapacitet att hantera den invecklade kemin i koordinationsburar. Däremot var träningen på de organiska liganderna (länkarna) framgångsrik, vilket betonar fördelarna med att fokusera på mindre byggstenar. Dock är fördelarna med detta projekt betydande. Den kunskap som förvärvats om hur generativa modeller fungerar och den komplexa världen av supramolekylär kemi har gett en unik möjlighet att förstå utmaningarna och möjligheterna med att tillämpa GenAI på ett så komplicerat område. Erfarenheterna har visat på behovet av ytterligare förfining av datahantering och modellträningstekniker, vilket banar väg för mer avancerade tillämpningar i framtiden. Det här projektet har inte bara ökat vår förståelse för GenAI:s möjligheter och begränsningar i koordinationsburar utan också lagt grunden för framtida forskning som i slutändan kan leda till banbrytande upptäckter i utformningen av nya burstrukturer. Ytterligare studier skulle kunna fokusera på att lära sig från länkarna för att hjälpa framtida datadrivna projekt för burdesign.

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