We report for the first time a broad equilibrium model describing the complexation of ionic species in non-aqueous media that explicitly includes ion pairing for one of the components and that relies upon activities rather than molar concentrations. This model directly contradicts existing commonplace equilibrium treatments, which were shown to be incomplete, often invalid, and misleading. Experimental validation of our model was achieved through studies of pseudorotaxane formation between dibenzylammonium salts (DBAm-X) and dibenzo-24-crown-8 (DB24C8) in CDCl3:CD3CN (3:2). In that particular case, we showed that fluctuations in the apparent Ka,exp values as usually reported are attributable to ion pairing, with a dissociation constant Kipd, and that the constant Kassoc for pseudorotaxane complexation is independent of the counterion, a result of the complex existing in solution as a free cation. In accord with this model, we further described a straightforward and simple method to increase the extent of complexation by using either a ditopic cation and anion host, or adding to the charged host/guest solution a molecularly separate host capable of complexing the dissociated counterion. Also in accord with this model, we investigated the influence of the solvent¡¯s dielectric constant on Kipd and Kassoc. On the basis of competing condensation reactions between amines and ketones which were shown to occur within the timescale of host/guest recognition, we also challenged the commonly employed use of acetone in similar complexation studies involving 2o ammonium ions. Because a major goal of this work was to ultimately increase binding efficiency and selectivity, we explored new methods to drive complexation in related pseudorotaxane systems. We noted that addition of di- or tri-topic hydrogen bond accepting anions to solutions of bis(5-hydroxymethyl-1,3-phenylene)-32-crown-10 or bis(5-carboxy-1,3-phenylene)-32-crown-10 and paraquat di(hexafluorophosphate) served to significantly enhance host/guest interaction. The addition of Et4N+TFA- to an acetone solution of diacid crown and paraquat 2PF6 effectively boosted Ka,exp 40-fold, as estimated by 1H NMR studies. Similar increases in the apparent Ka,exp were observed upon the addition of n-Bu4N+OTs-. Evidenced by crystal structures, the increase in association resulted from chelation of the OH moieties of the crown by the di- or tri-topic anions, forming supramolecular bicyclic macrocycles (pseudocryptands) and stabilizing the complex in a cooperative manner. Significantly, Ka,exp of one of the pseudocryptands was shown to equal that determined in the corresponding cryptand complex. / Ph. D.

Yes / The possibility of using differential pre‐heating prior to supramolecular gelation to control the balance between hydrogen‐bonding and aromatic stacking interactions in supramolecular gels and obtain consequent systematic regulation of structure and properties is demonstrated. Using a model aromatic peptide amphiphile, Fmoc‐tyrosyl‐leucine (Fmoc‐YL) and a combination of fluorescence, infrared, circular dichroism and NMR spectroscopy, it is shown that the balance of these interactions can be adjusted by temporary exposure to elevated temperatures in the range 313–365 K, followed by supramolecular locking in the gel state by cooling to room temperature. Distinct regimes can be identified regarding the balance between H‐bonding and aromatic stacking interactions, with a transition point at 333 K. Consequently, gels can be obtained with customizable properties, including supramolecular chirality and gel stiffness. The differential supramolecular structures also result in changes in proteolytic stability, highlighting the possibility of obtaining a range of supramolecular architectures from a single molecular structure by simply controlling the pre‐assembly temperature. / FP7 Ideas: European Research Council. Grant Number: 258775

In the last 20 years there has been a number of synthetic and natural product based molecular replicators published in the literature. The majority of these systems have focused on the minimal model with only a few examples of cross-catalytic or reciprocal replication. Of the cross-catalytic systems investigated the majority focus around the use of natural products, oligonucleotides, peptides etc. This thesis will investigate the design, synthesis and kinetic analysis of both synthetic minimal and reciprocal replicating systems, and how these two forms of replication interact in a complex hypercyclic network. Chapter 1 introduces key concepts such as molecular recognition, intramolecularity/ enzyme kinetic, bisubstrate systems and the work conducted into replication systems to date. Chapter 2 describes the design, synthesis and kinetic analysis of a reciprocal replicating system, based on Diels-Alder and 1,3-dipolar cycloadditions, before going on to discuss what we have learned and how this system can be improved. Chapter 3 focuses on the design, synthesis and kinetic analysis of a replicating network (minimal and reciprocal replication), based on 1,3-dipolar cycloadditions. Initial individual systems are examined in isolation to determine their behavior and nature. After which the systems are combined to observe how each species interacts in a potential complex hypercyclic network. Chapter 4 investigates the redesign of the replicating network in Chapter 3 in order to overcome the problems identified from its kinetic analysis. Chapter 5 introduces the shift in direction away from kinetically controlled replicating networks towards systems in thermodynamic equilibrium.

In the last twenty years, chemists have devised numerous synthetic chemical systems in which self-replication operates, demonstrating that molecules can replicate themselves without the aid of enzymes and that self-replication is not a prerogative of nucleic acids only. However, the coupling of replication to other recognition-mediated events and its exploitation in the amplification of large supramolecular assemblies, such as mechanically interlocked molecules, have remained unexplored areas. Among mechanically interlocked molecules, rotaxanes represent particularly attractive targets because of their application as molecular switches. This thesis describes how the recognition-mediated synthesis of a rotaxane can be combined to the amplification of its structure by replication. Kinetic models for the integration of self-replication with the formation of a rotaxane are presented. The logical steps required to convert these models into molecular structures through consideration of the design criteria highlighted by the models are discussed and executed. The macrocyclic component is an essential part of a rotaxane. The synthesis of several novel macrocycles is presented. Their ability to bind guests in their cavities through hydrogen bonds was probed. The best macrocycle/guest pairs were integrated in the formation of rotaxanes. Further investigations on the stoppering reaction and on the various recognition processes involved in the system lead ultimately to the construction of self-replicating rotaxanes.

No description available.

O trabalho apresentado nesta Tese tem como objetivo a elaboração de estruturas polinucleares baseadas em clusters trinucleares de rutênio. Os oligômeros estudados são opções interessantes para o desenvolvimento futuro de dispositivos supramoleculares, em função de suas propriedades fotofísicas e eletroquímicas. Um trímero e uma série de dímeros mistos foram obtidos pela combinação do cluster [Ru3O(CH3COO)6(py)2(CH3OH)]+ com complexos [Ru(bpy)2(P)(L)]+ (P = ligante de ponte N-heterocíclico; L = P, Cl ou CN). A caracterização por RMN, voltametria cíclica e espectroeletroquímica dos dímeros onde L = Cl foi utilizada como base na interpretação dos resultados obtidos para os demais complexos; os dados refletem uma interação fraca entre os fragmentos, que depende das características eletrônicas da ponte P. Nos dímeros onde L = CN, ocorre a supressão da emissão do cromóforo [Ru(bpy)2] pelo cluster através de um mecanismo de transferência de elétrons fotoinduzida. Para o cluster na forma reduzida, sugere-se também a ocorrência de transferência de energia. Na segunda parte da Tese, são apresentados sistemas policlusters contendo seis e dez unidades ligadas em ponte. As novas supermoléculas apresentam uma série de processos redox multieletrônicos e, neste caso, a comunicação eletrônica entre os centros metálicos é mais pronunciada, sendo dependente do estado de oxidação dos clusters. / The aim of the work reported is to develop polynuclear structures based on trinuclear ruthenium clusters. All the oligomers are seen as interesting options to the future development of supramolecular devices, due to their photophysical and electrochemical properties. A series of mixed dimers and one trimer were obtained by the combination of the [Ru3O(CH3COO)6(py)2(CH3OH)]+ cluster with [Ru(bpy)2(P)(L)]+ complexes (P = N-heterocyclic bridging ligand; L = P, Cl or CN). The NMR, cyclic voltammetry and spectroelectrochemical characterization of the dimers where L = Cl were used as a base to interpret the results collected for the other complexes; the data reflect a weak interaction between the units, depending on the electronic characteristics of the bridging ligand P. In the dimers where L = CN, occurs the quenching of the [Ru(bpy)2] emission by the cluster through a photoinduced electron transfer mechanism. For the cluster in its reduced form, it is suggested that an energy transfer process also occurs. On the second part of the Thesis, polycluster systems containing six and ten bridged cluster units are reported. The novel supermolecules present a series of multielectronic redox processes and, in this case, electronic communication among the metallic centers is more pronounced, depending on the clusters oxidation state.

[Truncated abstract] The scientific endeavours described within this thesis attempt to create novel solutions to current scientific, commercial and industrial downfalls, and contribute to the advancement of technologies in these areas. This has been achieved through the application of theoretical and experimental principles, entrenched in the domains of chemistry and physics, which have been harnessed to assist in the transformation from nanoscience to nanotechnology. These solutions range from unique supramolecular systems capable of selective-diameter enrichment of single-walled carbon nanotubes (SWCNTs), to the fabrication of low-cost, potentially remote deployable carbon nanotube-based gas and vapour sensors, and expand right through to the development of water-soluble fluoroionophoric sensors and manipulations of a molecular form of carbon in constructing all-carbon nano-architectures. For the advancement and successful integration of carbon nanotubes (CNTs) into commercial processes, the advent of scalable separation protocols based on their electronic properties is required. SWCNTs have been successfully solubilised using water-soluble p-phosphonated calix[n]arenes (n = 4, 6, 8) and 'extended arm' upper rim functionalised (benzyl, phenyl) p-sulfonated calix[8]arenes. Selective SWCNT diameter solubilisation has been demonstrated and subsequent preferential enrichment of SWCNTs with semiconducting or metallic electronic properties has been achieved. In addition, semiconducting nanotube-enriched supernatants (liquid) have been utilised to fabricate on/off field effect transistors (FET). These water-soluble supramolecular systems can be incorporated into post-growth purification protocols, with direct implications in areas such as carbon nano-electronics and device fabrication. In the current global environment there is a heightened level of public and governmental disquiet due to the reality of impending terrorist attacks. This is compounded by the inherent ease of manufacture and effectiveness of specific chemical warfare agents (CWAs) used in small-scale terrorist operations. ... Additional all-carbon structures are described with the formation of rings of helical SWCNT bundles through post-growth SWCNT modifications, and a variety of fibrous all-carbon structures, most notably novel square-geometry carbon nano-fibres (CNFs), through catalytic-chemical vapour deposition (C-CVD) synthesis strategies. The current requirement for entirely water-soluble fluorescent sensors is routinely documented in the literature. The autofluorescence properties of p-phenyl-sulfonated calix[8]arene are characterised and this water-soluble cavitand is surveyed as a metal cation sensor candidate. This particular system was found to exhibit a change in fluorescence response when exposed to divalent metal cations, and interactions with [UO2]2+, Pb2+, Co2+, and Cu2+ ions are discussed in detail. The system is characterised through a variety of analytical techniques to yield sensor calibration data, degradation characteristics, pH sensitivity and suitability as a 'small molecule' drug-carrier.

The development of selective and sensitive sensors for anionic species in water is a growing field of research. In particular, the detection of fluoride in aqueous samples is of great interest because of health related problems attributed to this anion. Furthermore its small size and its high hydration energy make it a particularly <p>challenging species to recognize in water. <p>Uranyl-salophen receptors have shown to be good receptors for this anion in organic solvents due to their hard Lewis acid character which makes them good binders for the hard Lewis base fluoride. However they are not water soluble. <p>The incorporation of uranyl-salophen receptors 1-3 within cationic micelles (CTABr and CTACl) will make them “water-compatible” and give us the possibility to study the behaviour of these system in water. The 3 receptors shown <p>in figure 1 were studied in this thesis. Preliminary work had already been reported on receptor 1 in CTABr micelles. Binding affinities studies showed that these receptors have binding constants for fluoride of the order of 104 M−1 which is two orders of magnitude higher than <p>the value obtained for the same receptors in a less competitive solvent such as methanol. This suggests that the micellar environment has an effect, not only on the solubility of the receptors in water, but also for the binding process. <p>Physico-chemical studies were undertaken on the system in order to obtain some structural informations. Dynamic Light Scattering experiments showed an increase in the size of the CTABr micelles upon receptor’s incorporation but not on the CTACl ones. <p>NMR studies, including chemical shift variation measurements, nOe and Paramagnetic Relaxation Enhancement (PRE) experiments, were undertaken in order to analyse the location and orientation of the receptors in the micelles. Results indicate that receptor 1 is located at the micellar surface, in CTABr micelles and a little deeper in CTACl micelles, orienting the receptors binding site towards the exterior of the micelle. Receptor 2 is more buried inside the micelles compared to receptor 1 but with a similar orientation. Receptor 3 is the most deeply buried <p>in the micelles, and the experiments suggests that no preferential orientation is adopted. <p>A systematic study of the factors affecting PRE measurements was also undertaken showing the dependency of this measurements on the surfactant concentration, the nature of the counterion and the ionic force. A method, based on the normalization of the relaxivity values to the value obtained for the micelle polar head is proposed in order to avoid all the variations due to the experimental conditions and thus enabling the comparison of different systems. / Doctorat en Sciences de l'ingénieur / info:eu-repo/semantics/nonPublished

Doctor of Philosophy / Department of Chemistry / Christer B. Aakeroy / The ability to predict and control molecular arrangements without compromising the individual molecules themselves still remains an important goal in supramolecular chemistry. This can be accomplished by establishing a hierarchy of intermolecular interactions such as hydrogen and halogen bond, which may facilitate supramolecular assembly processes. Several acetaminopyridine/acetaminomethylpyridine supramolecular reactants (SR’s) were prepared with aliphatic carboxylic acids in order to determine patterns of molecular recognition preferences of the N-H moiety. The results obtained revealed the formation of molecular cocrystals through heteromeric O-H…N/N-H…O hydrogen bonds with the acetaminopyridine/acetaminomethylpyridine binding site. Furthermore, the SR’s also reacted with metal ions resulting in robust 1D and 2D metal-containing architectures. A series of pyridyl/pyrazine mono-N-oxide compounds were synthesized and reacted with a variety of halogenated benzoic acids, in order to assess the ability of these molecules to establish binding selectivity when both a hydrogen and halogen bond donor is present. The results obtained revealed that the pyridyl/carboxylic acid synthon formed 7/7 times and halogen bonds (N-O…I or N-O…Br) extended the SR/acid dimers into 1D and 2D networks. These results were rationalized via charge calculations as well as through the hierarchical view of intermolecular interactions consisting of hydrogen and halogen bonds. Furthermore, a series of thienyl compounds were synthesized and allowed to react with halogen bond donors to determine whether the halogen bond is purely electrostatic or based on the hard and soft acids and bases principles. The results obtained showed that of the 34 reactions between a halogen bond donor and thienyl compounds, the halogen bond is predominantly electrostatic in nature. Finally, as a result of our improved understanding on molecular recognition, we were able to carry out systematic structure-property studies on a series of cocrystals of anti-cancer drug molecules with aliphatic carboxylic acids. This study revealed that systematic changes to the molecular nature of the co-crystallizing agent combined with control over the way individual building blocks are organized within the crystalline lattice makes it possible to establish predictable links between molecular structure and macroscopic physical properties, such as melting behavior, solubility, dissolution rate, etc.

Doctor of Philosophy / Department of Chemistry / Christer B. Aakeroy / Supramolecular synthesis relies upon the creative and rational use of the common intermolecular forces and a proper understanding of these forces is critical for design and assembly of molecular building blocks into extended networks. The strength of seven substituted pyridines as hydrogen-bond acceptors was probed using a series of fifteen mono/dicarboxylic acids to demonstrate the interrelationship between the charge on the substrate and its ability to form co-crystals/salts. The higher charge in the acceptor led to proton transfer (100% yield) from the hydrogen bond donor to give a salt, whereas the lower charge led to co-crystals. This specificity observed for small molecules was extended to an investigation of selectivity in ditopic molecules. A series of nineteen hydrogen-bond donors, including fifteen carboxylic acids and four cyanoximes, were tested for binding preferences against ten ditopic ligands with variable charges. The overall supramolecular yield of 82% (9/11) proved a high degree of reliability in terms of best acceptor/donor approach, hence establishing the efficiency of the calculated charges as a guideline for molecular recognition processes. Solubility and thermal properties of pharmaceutical drug mimics were altered via formation of co-crystals/salts. The ligands and their co-crystals/salts with five even-chain dicarboxylic acids were synthesized and their comparative solubility in pure water and in pH 6.8 buffer solution measured. Solubility enhancement to a degree of 9x is observed for pharmaceutical drug haloperidol, whereas decrease in solubility down to 81% is achieved for 2-amino-5-(3-pyridyl)pyrimidine (which has agrochemical significance). Also the thermal and solubility behavior of these co-crystals were shown to reflect the properties of their parent co-crystallizing agents, allowing for a modulation of physical properties. Finally, the specificity and selectivity of the intermolecular interactions observed for small molecules were applied in the synthesis of hydrogen and halogen-bonded capsules. Several resorcinarene-based cavitands were synthesized and their upper rim decorated with acetamidopyridyl, aminopyrazinyl, 3-pyridyl, and 4-pyridyl moieties with hydrogen and halogen-bonding potentials. A homomeric hydrogen-bonded capsule was formed with self-assembly of acetamidoethynylcavitand via N-H···O=C interactions, whereas a heteromeric halogen-bonded capsule, the very first of its kind, was formed with N···I halogen-bonded interaction between 3-pyridylcavitand and tetrafluoroiodo-substituted calixarene.