Retro and retroenantio analogs of cecropin-melittin hybrids.

Hybrid analogs of cecropin A (CA) and melittin (M), which are potent antibacterial peptides, have been synthesized. To understand the structural requirements for this antibacterial activity, we have also synthesized the enantio, retro, and retroenantio isomers of two of the hybrids and their N-terminally acetylated derivatives. All analogs of CA(1-13)M(1-13)-NH2 were as active as the parent peptide against five test bacterial strains, but one bacterial strain was resistant to the retro and retroenantio derivatives. Similarly, all analogs of CA(1-7)M(2-9)-NH2 were active against four strains, while two strains were resistant to the retro and retroenantio analogs containing free NH3+ end groups, but acetylation restored activity against one of them. From these data it was concluded that chirality of the peptide was not a critical feature, and full activity could be achieved with peptides containing either all L- or all D-amino acids in their respective right-handed or left-handed helical conformations. For most of the bacterial strains, the sequence of these peptides or the direction of the peptide bonds could be critical but not both at the same time. For some strains, both needed to be conserved.

Phosphonate and quinoxaline cavitands for molecular recognition and sensing

In the last decade, phosphonate and quinoxaline cavitand have been extensively studied, highlighting their outstanding recognition properties. Their successful applications in material science and sensing open the way to new potential applications, such as border security, environmental monitoring and chiral recognition. The present thesis explores the recognition properties of phosphonate and quinoxaline cavitands towards new targets, for molecular recognition and sensing applications. Chapter 2 highlights the enantioselective behavior of phosphonate cavitands towards chiral guests in the solid state and in solution. Phosphonate cavitands were exploited for the molecular recognition of L-lactic acid (chapter 3), a widespread natural molecule which offer multiple potential applications, and a human sweat marker used for the detection of human presence (chapter 4). The second part is devoted to sensing applications of quinoxaline cavitands. Chapter 5 describes the use of QxCav for the preconcentration of drugs precursors, while chapter 6 reports the design, synthesis and grafting of a rigidified EtQxBox on a silicon wafer.

Impurity states in the quantum spin Hall phase in graphene

Two-dimensional insulators with time-reversal symmetry can have two topologically different phases, the quantum spin Hall and the normal phase. The former is revealed by the existence of conducting edge states that are topologically protected. Here we show that the reaction to impurity, in bulk, is radically different in the two phases and can be used as a marker for the topological phase. Within the context of the Kane-Mele model for graphene, we find that strictly normalizable in-gap impurity states only occur in the quantum spin Hall phase and carry a dissipationless current whose chirality is determined by the spin and pseudospin of the residing electron.

Electrochemical behaviour of different redox probes on single wall carbon nanotube buckypaper-modified electrodes

In the present work, the electrochemical properties of single-walled carbon nanotube buckypapers (BPs) were examined in terms of carbon nanotubes nature and preparation conditions. The performance of the different free-standing single wall carbon nanotube sheets was evaluated via cyclic voltammetry of several redox probes in aqueous electrolyte. Significant differences are observed in the electron transfer kinetics of the buckypaper-modified electrodes for both the outer- and inner-sphere redox systems. These differences can be ascribed to the nature of the carbon nanotubes (nanotube diameter, chirality and aspect ratio), surface oxidation degree and type of functionalities. In the case of dopamine, ferrocene/ferrocenium, and quinone/hydroquinone redox systems the voltammetric response should be thought as a complex contribution of different tips and sidewall domains which act as mediators for the electron transfer between the adsorbate species and the molecules in solution. In the other redox systems only nanotube ends are active sites for the electron transfer. It is also interesting to point out that a higher electroactive surface area not always lead to an improvement in the electron transfer rate of various redox systems. In addition, the current densities produced by the redox reactions studied here are high enough to ensure a proper electrochemical signal, which enables the use of BPs in sensing devices.

THE DESIGN AND SYNTHESIS OF SILOXANE PRECURSORS FOR CHIRAL PERIODIC MESOPOROUS ORGANOSILICA MATERIALS

The development of cost-effective and reliable methods for the synthesis and separation of asymmetric compounds is paramount in helping to meet society’s ever-growing demand for chiral small molecules. Of these methods, chiral heterogeneous supports are particularly appealing as they allow for the reuse of the chiral source. One such support, based on the synergy between chiral organic units and structurally stable inorganic silicon scaffolds are periodic mesoporous organosilicas (PMOs). In the work described herein, I examine some of the factors governing the transmission of chirality between chiral dopants and prochiral bulk phases in chiral PMO materials. In particular, the exploration of 1,1’-binaphthalene-bridged chiral dopants with a focus on the point of attachment into the materials. Moreover, the effects of ordering in the materials are examined and reveal that chirality transfer is more facile in materials with molecular-scale order then those containing amorphous walls. Secondly, the issues surrounding the synthesis and purification of aryl-triethoxysilanes as siloxane precursors are addressed. Both the introduction of a two-carbon linker and the direct attachment of allyl and mixed allyldiethoxysilane species are explored. This work demonstrates that allyldiethoxysilanes are ideal, in that they are stable enough to permit facile synthesis, while still being able to hydrolyze completely to produce well-ordered materials. Lastly, the production of new bulk phases for chiral PMO materials is examined by introducing new prochiral nitrogen-containing siloxane precursors. Biphenyldiamine and bipyridine-bridged siloxane precursors are readily synthesized on reasonable scales. Their use as the bulk siloxane precursor in the production of PMO materials however, is precluded by insufficient gelation and additional siloxane precursors are necessary for the production of ordered materials. In addition to the research detailed above that forms the body of this thesis, two short works are appended. The first details the production of polythiophene assemblies mediated through coordination nanospaces, while the second explores the production of N-heterocyclic carbene functionalized gold nanoparticles through ligand exchange.

Novel one-dimensional structures and solution behaviour of copper(II) bromide and chloride complexes of a new pentapyridyldiamine ligand

Copper(II) bromide and chloride complexes of the new heptadentate ligand 2,6-bis(bis(2-pyridylmethyl)amino)methylpyridine (L) have been prepared. For the bromide complexes, chains of novel, approximately C-2-symmetric, chiral [Cu-2(L)Br-2](2+) 'wedge-shaped' tectons are found. The links between the dicopper tectons and the overall chirality and packing of the chains are dictated by the bromide ion content, not the counter anion. In contrast, the chloride complexes exhibit linked asymmetric [Cu-2(L)Cl-3](+) tectons with distinct N3CuCl2 and N4CuCl2 centres in the solid. The overall structures of the dicopper bromide and chloride units persist in solution irrespective of the halide. The redox chemistry of the various species is also described.

Non-classical inhibitors of dihydrofolate reductase

This thesis comprises two main objectives. The first objective involved the stereochemical studies of chiral 4,6-diamino-1-aryl-1,2-dihydro-s-triazines and an investigation on how the different conformations of these stereoisomers may affect their binding affinity to the enzyme dihydrofolate reductase (DHFR). The ortho-substituted 1-aryl-1,2-dihydro-s-triazines were synthesised by the three component method. An ortho-substitution at the C6' position was observed when meta-azidocycloguanil was decomposed in acid. The ortho-substituent restricts free rotation and this gives rise to atropisomerism. Ortho-substituted 4,6-diamino-1-aryl-2-ethyl-1,2-dihydro-2-methyl-s-triazine contains two elements of chirality and therefore exists as four stereoisomers: (S,aR), (R,aS), (R,aR) and (S,aS). The energy barriers to rotation of these compounds were calculated by a semi-empirical molecular orbital program called MOPAC and they were found to be in excess of 23 kcal/mol. The diastereoisomers were resolved and enriched by C18 reversed phase h.p.l.c. Nuclear overhauser effect experiments revealed that (S,aR) and (R,aS) were the more stable pair of stereoisomers and therefore existed as the major component. The minor diastereoisomers showed greater binding affinity for the rat liver DHFR in in vitro assay. The second objective entailed the investigation into the possibility of retaining DHFR inhibitory activity by replacing the classical diamino heterocyclic moiety with an amidinyl group. 4-Benzylamino-3-nitro-N,N-dimethyl-phenylamidine was synthesised in two steps. One of the two phenylamidines indicated weak inhibition against the rat liver DHFR. This weak activity may be due to the failure of the inhibitor molecule to form strong hydrogen bonds with residue Glu-30 at the active site of the enzyme.

Observed and predicted hydrogen bond motifs in crystal structures of hydantoins, dihydrouracils and uracils

A survey of crystal structures containing hydantoin, dihydrouracil and uracil derivatives in the Cambridge Structural Database revealed four main types of hydrogen bond motifs when derivatives with extra substituents able to interfere with the main motif are excluded. All these molecules contain two hydrogen bond donors and two hydrogen bond acceptors in the sequence of NH, C = O, NH, and C=O groups within a 5-membered ring (hydantoin) and two 6-membered rings (dihydrouracil and uracil). In all cases, both ring NH groups act as donors in the main hydrogen bond motif but there is an excess of hydrogen bond acceptors (two C=O able to accept twice each) and so two possibilities are found: (i) each carbonyl O atom may accept one hydrogen bond or (ii) one carbonyl O atom may accept two hydrogen bonds while the other does not participate in the hydrogen bonding. We observed different preferences in the type and symmetry of the motifs adopted by the different derivatives, and a good agreement is found between motifs observed experimentally and those predicted using computational methods. We identified certain molecular factors such as chirality, substituent size and the possibility of C-H⋯O interactions as important factors influencing the motif observation. © 2012 The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.

A sensing mechanism for the detection of carbon nanotubes using selective photoluminescent probes based on ionic complexes with organic dyes

The multifunctional properties of carbon nanotubes (CNTs) make them a powerful platform for unprecedented innovations in a variety of practical applications. As a result of the surging growth of nanotechnology, nanotubes present a potential problem as an environmental pollutant, and as such, an efficient method for their rapid detection must be established. Here, we propose a novel type of ionic sensor complex for detecting CNTs – an organic dye that responds sensitively and selectively to CNTs with a photoluminescent signal. The complexes are formed through Coulomb attractions between dye molecules with uncompensated charges and CNTs covered with an ionic surfactant in water. We demonstrate that the photoluminescent excitation of the dye can be transferred to the nanotubes, resulting in selective and strong amplification (up to a factor of 6) of the light emission from the excitonic levels of CNTs in the near-infrared spectral range, as experimentally observed via excitation-emission photoluminescence (PL) mapping. The chirality of the nanotubes and the type of ionic surfactant used to disperse the nanotubes both strongly affect the amplification; thus, the complexation provides sensing selectivity towards specific CNTs. Additionally, neither similar uncharged dyes nor CNTs covered with neutral surfactant form such complexes. As model organic molecules, we use a family of polymethine dyes with an easily tailorable molecular structure and, consequently, tunable absorbance and PL characteristics. This provides us with a versatile tool for the controllable photonic and electronic engineering of an efficient probe for CNT detection.

Controlled growth of carbon nanotubes for high performance nanoelectronics

Unique electrical and mechanical properties of single-walled carbon nanotubes (SWNTs) have made them one of the most promising candidates for next-generation nanoelectronics. Efficient utilization of the exceptional properties of SWNTs requires controlling their growth direction (e.g., vertical, horizontal) and morphologies (e.g., straight, junction, coiled). ^ In this dissertation, the catalytic effect on the branching of SWNTs, Y-shaped SWNTs (Y-SWNTs), was investigated. The formation of Y-shaped branches was found to be dependent on the composition of the catalysts. Easier carbide formers have a strong tendency to attach to the sidewall of SWNTs and thus enhance the degree of branching. Y-SWNTs based field-effect transistors (FETs) were fabricated and modulated by the metallic branch of the Y-SWNTs, exhibiting ambipolar characteristics at room temperature. A subthreshold swing of 700 mV/decade and an on/off ratio of 105 with a low off-state current of 10-13 A were obtained. The transport phenomena associated with Y- and cross-junction configurations reveals that the conduction mechanism in the SWNT junctions is governed by thermionic emission at T > 100 K and by tunneling at T < 100 K. ^ Furthermore, horizontally aligned SWNTs were synthesized by the controlled modification of external fields and forces. High performance carbon nanotube FETs and logic circuit were demonstrated utilizing the aligned SWNTs. It is found that the hysteresis in CNTFETs can be eliminated by removing absorbed water molecules on the CNT/SiO2 interface by vacuum annealing, hydrophobic surface treatment, and surface passivation. SWNT “serpentines” were synthesized by utilization of the interaction between drag force from gas flow and Van der Waals force with substrates. The curvature of bent SWNTs could be tailored by adjusting the gas flow rate, and changing the gas flow direction with respect to the step-edges on a single-crystal quartz substrate. Resistivity of bent SWNTs was observed to increase with curvature, which can be attributed to local deformations and possible chirality shift at curved part. ^ Our results show the successful synthesis of SWNTs having controllable morphologies and directionality. The capability of tailoring the electrical properties of SWNTs makes it possible to build an all-nanotube device by integrating SWNTs, having different functionalities, into complex circuits. ^

Design, Synthesis, and Photophysical Investigation of Porphyrin-containing Polymer-wrapped Single-walled Carbon Nanotubes

Significant advances in understanding the fundamental photophysical behavior of single-walled carbon nanotubes (SWNTs) have been made possible by the development of ionic, conjugated aryleneethynylene polymers that helically wrap SWNTs with well-defined morphology. My contribution to this work was the design and synthesis of porphyrin-containing polymers and the photophysical investigation of the corresponding polymer-wrapped SWNTs. For these new constructs, the polymer acts as more than just a solubilization scaffold; such assemblies can provide benchmark data for evaluating spectroscopic signatures of energy and charge transfer events and lay the groundwork for further, rational development of polymers with precisely tuned redox properties and electronic coupling with the underlying SWNT. The first design to incorporate a zinc porphyrin into the polymer backbone, PNES-PZn, suffered from severe aggregation in solution and was redesigned to produce the porphyrin-containing polymer S-PBN-PZn. This polymer was utilized to helically wrap chirality-enriched (6,5) SWNTs, which resulted in significant quenching of the porphyrin-based fluorescence. Time-resolved spectroscopy revealed a simultaneous rise and decay of the porphyrin radical cation and SWNT electron polaron spectroscopic signatures indicative of photoinduced electron transfer. A new polymer, S-PBN(b)-Ph2PZn3, was then synthesized which incorporated a meso-ethyne linked zinc porphyrin trimer. By changing the absorption profile and electrochemical redox potentials of the polymer, the photophysical behavior of the corresponding polymer-wrapped (6,5)-SWNTs was dramatically changed, and the polymer-wrapped SWNTs no longer showed evidence for photoinduced electron transfer.

New methods for the asymmetric synthesis of α-alkylated ketones and 1,3-amino alcohols

A large number of optically active drugs and natural products contain α-functionalised ketones or simple derivatives thereof. Furthermore, chiral α-alkylated ketones are useful synthons and have found widespread use in total synthesis. The asymmetric alkylation of ketones represents one of the most powerful and longstanding procedures in organic chemistry. Surprisingly, however, only one effective methodology is available, and this involves the use of chiral auxiliaries. This is discussed in Chapter 1, which also provides a background of other key topics discussed throughout the thesis. Expanding on the existing methodology of chiral auxiliaries, Chapter 2 details the synthesis of a novel chiral auxiliary containing a pyrrolidine ring and its use in the asymmetric preparation of α-alkylated ketones with good enantioselectivity. The synthesis of racemic α-alkylated ketones as reference standards for GC chromatography is also reported in this chapter. Chapter 3 details a new approach to chiral α-alkylated ketones using an intermolecular chirality transfer methodology. This approach employs the use of simple non-chiral dimethylhydrazones and their asymmetric alkylation using the chiral diamine ligands, (+)- and (-)-sparteine. The methodology described represents the first example of an asymmetric alkylation of non-chiral azaenolates. Enantiomeric ratios up to 83 : 17 are observed. Chapter 4 introduces the first aldol-Tishchenko reaction of an imine derivative for the preparation of 1,3-aminoalcohol precursors. 1,3-Aminoalcohols can be synthesised via indirect routes involving various permutations of stepwise construction with asymmetric induction. Our approach offers an alternative highly diastereomeric route to the synthesis of this important moiety utilising N-tert-butanesulfinyl imines in an aldol-Tishchenko-type reaction. Chapter 5 details the experimental procedures for all of the above work. Chapter 6 discusses the results of a separate research project undertaken during this PhD. 2-alkyl-quinolin-4-ones and their N-substituted derivatives have several important biological functions such as the role of Pseudomonas quinolone signal (PQS) in quorum sensing. Herein, we report the synthesis of its biological precursor, 2-heptyl-4-hydroxy-quinoline (HHQ) and possible isosteres of PQS; the C-3 Cl, Br and I analogues. N-Methylation of the iodide was also feasible and the usefulness of this compound showcased in Pd-catalysed cross-coupling reactions, thus allowing access to a diverse set of biologically important molecules.

The development of novel chiral tethers for controlling intramolecular aryl-aryl coupling and their application in the synthesis of gomisin M1 and analogues

The primary focus of this thesis was the development of a novel chiral tether that could be used to control axial chirality around a newly formed aryl-aryl bond, and the extension of this methodology to the model synthesis of gomisin M1. In chapter 1, a review detailing the use of chiral tethers in the synthesis of atropisomers is discussed. The use of a variety of chiral molecules including 1,2-diols, 1,3-diols and other diol-based tethers, as well as amine-based and miscellaneous tethers are detailed. In chapter 2, the rationale behind the design of our novel molecular tethers, along with the subsequent synthesis of three chiral 1,3-diol-based tethers, is outlined. The method by which the enantiopurity of these diols was determined is also reviewed. This chapter also includes the attempted Mitsunobu and intramolecular couplings in the model synthesis of BINOL. Chapter 3 discusses the synthesis of suitable aryl halide substrates, and their employment in the attempted tether-controlled asymmetric model synthesis of gomisin M1. A comprehensive investigation into the attempted intramolecular biaryl coupling of these tethered substrates is also included. The non-stereoselective model synthesis of gomisin M1 is outlined in chapter 4. The installation of the desired biaryl linkage and the subsequent attempted intramolecular McMurry couplings are discussed. The impact of different protecting groups in the molecule on the intramolecular McMurry reaction is also outlined. Chapter 5 details the full experimental procedures, including spectroscopic and analytical data for the compounds prepared during this research.

THE DESIGN AND SYNTHESIS OF SILOXANE PRECURSORS FOR CHIRAL PERIODIC MESOPOROUS ORGANOSILICA MATERIALS

The development of cost-effective and reliable methods for the synthesis and separation of asymmetric compounds is paramount in helping to meet society’s ever-growing demand for chiral small molecules. Of these methods, chiral heterogeneous supports are particularly appealing as they allow for the reuse of the chiral source. One such support, based on the synergy between chiral organic units and structurally stable inorganic silicon scaffolds are periodic mesoporous organosilicas (PMOs). In the work described herein, I examine some of the factors governing the transmission of chirality between chiral dopants and prochiral bulk phases in chiral PMO materials. In particular, the exploration of 1,1’-binaphthalene-bridged chiral dopants with a focus on the point of attachment into the materials. Moreover, the effects of ordering in the materials are examined and reveal that chirality transfer is more facile in materials with molecular-scale order then those containing amorphous walls. Secondly, the issues surrounding the synthesis and purification of aryl-triethoxysilanes as siloxane precursors are addressed. Both the introduction of a two-carbon linker and the direct attachment of allyl and mixed allyldiethoxysilane species are explored. This work demonstrates that allyldiethoxysilanes are ideal, in that they are stable enough to permit facile synthesis, while still being able to hydrolyze completely to produce well-ordered materials. Lastly, the production of new bulk phases for chiral PMO materials is examined by introducing new prochiral nitrogen-containing siloxane precursors. Biphenyldiamine and bipyridine-bridged siloxane precursors are readily synthesized on reasonable scales. Their use as the bulk siloxane precursor in the production of PMO materials however, is precluded by insufficient gelation and additional siloxane precursors are necessary for the production of ordered materials. In addition to the research detailed above that forms the body of this thesis, two short works are appended. The first details the production of polythiophene assemblies mediated through coordination nanospaces, while the second explores the production of N-heterocyclic carbene functionalized gold nanoparticles through ligand exchange.

Optical properties of chiral thin films and microparticles

In this work I study the optical properties of helical particles and chiral sculptured thin films, using computational modeling (discrete dipole approximation, Berreman calculus), and experimental techniques (glancing angle deposition, ellipsometry, scatterometry, and non-linear optical measurements). The first part of this work focuses on linear optics, namely light scattering from helical microparticles. I study the influence of structural parameters and orientation on the optical properties of particles: circular dichroism (CD) and optical rotation (OR), and show that as a consequence of random orientation, CD and OR can have the opposite sign, compared to that of the oriented particle, potentially resulting in ambiguity of measurement interpretation. Additionally, particles in random orientation scatter light with circular and elliptical polarization states, which implies that in order to study multiple scattering from randomly oriented chiral particles, the polarization state of light cannot be disregarded. To perform experiments and attempt to produce particles, a newly constructed multi stage thin film coating chamber is calibrated. It enables the simultaneous fabrication of multiple sculptured thin film coatings, each with different structure. With it I successfully produce helical thin film coatings with Ti and TiO_{2}. The second part of this work focuses on non-linear optics, with special emphasis on second-harmonic generation. The scientific literature shows extensive experimental and theoretical work on second harmonic generation from chiral thin films. Such films are expected to always show this non-linear effect, due to their lack of inversion symmetry. However no experimental studies report non-linear response of chiral sculptured thin films. In this work I grow films suitable for a second harmonic generation experiment, and report the first measurements of non-linear response.