Supramolecular Organization of Heptapyrenotide Oligomers—An in Depth Investigation by Molecular Dynamics Simulations

We present a molecular modeling study based on ab initio and classical molecular dynamics calculations, for the investigation of the tridimensional structure and supramolecular assembly formation of heptapyrenotide oligomers in water solution. Our calculations show that free oligomers self-assemble in helical structures characterized by an inner core formed by π- stacked pyrene units, and external grooves formed by the linker moieties. The coiling of the linkers has high ordering, dominated by hydrogen-bond interactions among the phosphate and amide groups. Our models support a mechanism of longitudinal supramolecular oligomerization based on interstrand pyrene intercalation. Only a minimal number of pyrene units intercalate at one end, favoring formation of very extended longitudinal chains, as also detected by AFM experiment. Our results provide a structural explanation of the mechanism of chirality amplification in 1:1 mixtures of standard heptapyrenotides and modified oligomers with covalently linked deoxycytidine, based on selective molecular recognition and binding of the nucleotide to the groove of the left-wound helix.

Stereoselective synthesis and structure determination of a bicyclo[3.3.2]decapeptide

By analogy to the structural diversity of covalent bond networks between atoms within organic molecules, one can design topologically diverse peptides from mathematical graphs by assigning amino acids to graph nodes and peptide bonds to graph edges. The key is to use diamino acids or amino diacids as equivalents of trivalent graph nodes, which enables a variety of graph topologies beyond the standard linear and monocyclic graphs in natural peptides. Here the bicyclic decapeptide A1FGk2VFPE1AG2 (1b) was prepared and crystallized to assign its bridge stereochemistry. The bridge configuration appears as planned by the chirality of the branching amino acids. Bicyclization furthermore depends on the presence of matched chiralities in the branching amino acids. The stereoselective formation of the second bridge opens the way for the synthesis of a large family of bicyclic peptides as promising new scaffolds for drug design.

Metabolic profiling of praziquantel enantiomers

Praziquantel (PZQ), prescribed as a racemic mixture, is the most readily available drug to treat schistosomiasis. In the present study, ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-ESI-QTOFMS) based metabolomics was employed to decipher the metabolic pathways and enantioselective metabolic differences of PZQ. Many phase I and four new phase II metabolites were found in urine and feces samples of mice 24h after dosing, indicating that the major metabolic reactions encompassed oxidation, dehydrogenation, and glucuronidation. Differences in the formation of all these metabolites were observed between (R)-PZQ and (S)-PZQ. In an in vitro phase I incubation system, the major involvement of CYP3A, CYP2C9, and CYP2C19 in the metabolism of PZQ, and CYP3A, CYP2C9, and CYP2C19 exhibited different catalytic activity toward the PZQ enantiomers. Apparent Km and Vmax differences were observed in the catalytic formation of three mono-oxidized metabolites by CYP2C9 and CYP3A4 further supporting the metabolic differences for PZQ enantiomers. Molecular docking showed that chirality resulted in differences in substrate location and conformation, which likely accounts for the metabolic differences. In conclusion, in silico, in vitro, and in vivo methods revealed the enantioselective metabolic profile of praziquantel.

Excited state interactions between the chiral Au 38 L 24 cluster and covalently attached porphyrin

A protected S-acetylthio porphyrin was synthesized and attached to the Au38(2-phenylethanethiolate)24 cluster in a ligand exchange reaction. Chiral high performance liquid chromatography of the functionalized cluster yielded enantiomeric pairs of clusters probably differing in the binding site of the porphyrin. As proven by circular dichroism, the chirality was maintained. Exciton coupling between the cluster and the chromophore is observed. Zinc can be incorporated into the porphyrin attached to the cluster, as evidenced by absorption and fluorescence spectroscopy, however, the reaction is slow. Quenching of the chromophore fluorescence is observed, which can be explained by energy transfer from the porphyrin to the cluster. Transient absorption spectra of Au38(2-phenylethanethiolate)24 and the functionalized cluster probe the bleach of the gold cluster due to ground state absorption and the characteristic excited state absorption signals. Zinc incorporation does not have a pronounced effect on the photophysical behaviour. Decay times are typical for the molecular behaviour of small monolayer protected gold clusters.

Bridged bicyclic peptides as potential drug scaffolds: synthesis, structure, protein binding and stability

Double cyclization of short linear peptides obtained by solid phase peptide synthesis was used to prepare bridged bicyclic peptides (BBPs) corresponding to the topology of bridged bicyclic alkanes such as norbornane. Diastereomeric norbornapeptides were investigated by 1H-NMR, X-ray crystallography and CD spectroscopy and found to represent rigid globular scaffolds stabilized by intramolecular backbone hydrogen bonds with scaffold geometries determined by the chirality of amino acid residues and sharing structural features of β-turns and α-helices. Proteome profiling by capture compound mass spectrometry (CCMS) led to the discovery of the norbornapeptide 27c binding selectively to calmodulin as an example of a BBP protein binder. This and other BBPs showed high stability towards proteolytic degradation in serum.

Movimiento de paredes de dominio magnético en nanohilos con defectos controlados

La investigación realizada en este trabajo de tesis se ha centrado en el estudio de la generación, anclaje y desenganche de paredes de dominio magnético en nanohilos de permalloy con defectos controlados. Las últimas tecnologías de nanofabricación han abierto importantes líneas de investigación centradas en el estudio del movimiento de paredes de dominio magnético, gracias a su potencial aplicación en memorias magnéticas del futuro. En el 2004, Stuart Parkin de IBM introdujo un concepto innovador, el dispositivo “Racetrack”, basado en un nanohilo ferromagnético donde los dominios de imanación representan los "bits" de información. La frontera entre dominios, ie pared magnética, se moverían en una situación ideal por medio de transferencia de espín de una corriente polarizada. Se anclan en determinadas posiciones gracias a pequeños defectos o constricciones de tamaño nanométrico fabricados por litografía electrónica. El éxito de esta idea se basa en la generación, anclaje y desenganche de las paredes de dominio de forma controlada y repetitiva, tanto para la lectura como para la escritura de los bits de información. Slonczewski en 1994 muestra que la corriente polarizada de espín puede transferir momento magnético a la imanación local y así mover paredes por transferencia de espín y no por el campo creado por la corriente. Desde entonces muchos grupos de investigación de todo el mundo trabajan en optimizar las condiciones de transferencia de espín para mover paredes de dominio. La fracción de electrones polarizados que viaja en un hilo ferromagnético es considerablemente pequeña, así hoy por hoy la corriente necesaria para mover una pared magnética por transferencia de espín es superior a 1 107 A/cm2. Una densidad de corriente tan elevada no sólo tiene como consecuencia una importante degradación del dispositivo sino también se observan importantes efectos relacionados con el calentamiento por efecto Joule inducido por la corriente. Otro de los problemas científico - tecnológicos a resolver es la diversidad de paredes de dominio magnético ancladas en el defecto. Los diferentes tipos de pared anclados en el defecto, su quiralidad o el campo o corriente necesarios para desenganchar la pared pueden variar dependiendo si el defecto posee dimensiones ligeramente diferentes o si la pared se ancla con un método distinto. Además, existe una componente estocástica presente tanto en la nucleación como en el proceso de anclaje y desenganche que por un lado puede ser debido a la naturaleza de la pared que viaja por el hilo a una determinada temperatura distinta de cero, así como a defectos inevitables en el proceso de fabricación. Esto constituye un gran inconveniente dado que según el tipo de pared es necesario aplicar distintos valores de corriente y/o campo para desenganchar la pared del defecto. Como se menciona anteriormente, para realizar de forma eficaz la lectura y escritura de los bits de información, es necesaria la inyección, anclaje y desenganche forma controlada y repetitiva. Esto implica generar, anclar y desenganchar las paredes de dominio siempre en las mismas condiciones, ie siempre a la misma corriente o campo aplicado. Por ello, en el primer capítulo de resultados de esta tesis estudiamos el anclaje y desenganche de paredes de dominio en defectos de seis formas distintas, cada uno, de dos profundidades diferentes. Hemos realizado un análisis estadístico en diferentes hilos, donde hemos estudiado la probabilidad de anclaje cada tipo de defecto y la dispersión en el valor de campo magnético aplicado necesario para desenganchar la pared. Luego, continuamos con el estudio de la nucleación de las paredes de dominio magnético con pulsos de corriente a través una linea adyacente al nanohilo. Estudiamos defectos de tres formas distintas e identificamos, en función del valor de campo magnético aplicado, los distintos tipos de paredes de dominio anclados en cada uno de ellos. Además, con la ayuda de este método de inyección que es rápido y eficaz, hemos sido capaces de generar y anclar un único tipo de pared minimizando el comportamiento estocástico de la pared mencionado anteriormente. En estas condiciones óptimas, hemos estudiado el desenganche de las paredes de dominio por medio de corriente polarizada en espín, donde hemos conseguido desenganchar la pared de forma controlada y repetitiva siempre para los mismos valores de corriente y campo magnético aplicados. Además, aplicando pulsos de corriente en distintas direcciones, estudiamos en base a su diferencia, la contribución térmica debido al efecto Joule. Los resultados obtenidos representan un importante avance hacia la explotación práctica de este tipo de dispositivos. ABSTRACT The research activity of this thesis was focused on the nucleation, pinning and depinning of magnetic domain walls (DWs) in notched permalloy nanowires. The access to nanofabrication techniques has boosted the number of applications based on magnetic domain walls (DWs) like memory devices. In 2004, Stuart Parkin at IBM, conceived an innovative concept, the “racetrack memory” based on a ferromagnetic nanowire were the magnetic domains constitute the “bits” of information. The frontier between those magnetic domains, ie magnetic domain wall, will move ideally assisted by a spin polarized current. DWs will pin at certain positions due to artificially created pinning sites or “notches” fabricated with ebeam lithography. The success of this idea relies on the careful and predictable control on DW nucleation and a defined pinning-depinning process in order to read and write the bits of information. Sloncsewski in 1994 shows that a spin polarized current can transfer magnetic moment to the local magnetization to move the DWs instead of the magnetic field created by the current. Since then many research groups worldwide have been working on optimizing the conditions for the current induced DW motion due to the spin transfer effect. The fraction of spin polarized electrons traveling through a ferromagnetic nanowire is considerably small, so nowadays the current density required to move a DW by STT exceeds 1 107 A/cm2. A high current density not only can produce a significant degradation of the device but also important effects related to Joule heating were also observed . There are other scientific and technological issues to solve regarding the diversity of DWs states pinned at the notch. The types of DWs pinned, their chirality or their characteristic depinning current or field, may change if the notch has slightly different dimensions, the stripe has different thickness or even if the DW is pinned by a different procedure. Additionally, there is a stochastic component in both the injection of the DW and in its pinning-depinning process, which may be partly intrinsic to the nature of the travelling DW at a non-zero temperature and partly due to the unavoidable defects introduced during the nano-fabrication process. This constitutes an important inconvenient because depending on the DW type different values of current of magnetic field need to be applied in order to depin a DW from the notch. As mentioned earlier, in order to write and read the bits of information accurately, a controlled reproducible and predictable pinning- depinning process is required. This implies to nucleate, pin and depin always at the same applied magnetic field or current. Therefore, in the first chapter of this thesis we studied the pinning and depinning of DW in six different notch shapes and two depths. An statistical analysis was conducted in order to determine which notch type performed best in terms of pinning probability and the dispersion measured in the magnetic field necessary to depin the magnetic DWs. Then, we continued studying the nucleation of DWs with nanosecond current pulses by an adjacent conductive stripe. We studied the conditions for DW injection that allow a selective pinning of the different types of DWs in Permalloy nanostripes with 3 different notch shapes. Furthermore, with this injection method, which has proven to be fast and reliable, we manage to nucleate only one type of DW avoiding its stochastic behavior mentioned earlier. Having achieved this optimized conditions we studied current induced depinning where we also achieved a controlled and reproducible depinning process at always the same applied current and magnetic field. Additionally, changing the pulse polarity we studied the joule heating contribution in a current induced depinning process. The results obtained represent an important step towards the practical exploitation of these devices.

A synthetic all d-amino acid peptide corresponding to the N-terminal sequence of HIV-1 gp41 recognizes the wild-type fusion peptide in the membrane and inhibits HIV-1 envelope glycoprotein-mediated cell fusion

Recent studies demonstrated that a synthetic fusion peptide of HIV-1 self-associates in phospholipid membranes and inhibits HIV-1 envelope glycoprotein-mediated cell fusion, presumably by interacting with the N-terminal domain of gp41 and forming inactive heteroaggregates [Kliger, Y., Aharoni, A., Rapaport, D., Jones, P., Blumenthal, R. & Shai, Y. (1997) J. Biol. Chem. 272, 13496–13505]. Here, we show that a synthetic all d-amino acid peptide corresponding to the N-terminal sequence of HIV-1 gp41 (D-WT) of HIV-1 associates with its enantiomeric wild-type fusion (WT) peptide in the membrane and inhibits cell fusion mediated by the HIV-1 envelope glycoprotein. D-WT does not inhibit cell fusion mediated by the HIV-2 envelope glycoprotein. WT and D-WT are equally potent in inducing membrane fusion. D-WT peptide but not WT peptide is resistant to proteolytic digestion. Structural analysis showed that the CD spectra of D-WT in trifluoroethanol/water is a mirror image of that of WT, and attenuated total reflectance–fourier transform infrared spectroscopy revealed similar structures and orientation for the two enantiomers in the membrane. The results reveal that the chirality of the synthetic peptide corresponding to the HIV-1 gp41 N-terminal sequence does not play a role in liposome fusion and that the peptides’ chirality is not necessarily required for peptide–peptide interaction within the membrane environment. Furthermore, studies along these lines may provide criteria to design protease-resistant therapeutic agents against HIV and other viruses.

A 12R-lipoxygenase in human skin: Mechanistic evidence, molecular cloning, and expression

A recognized feature of psoriasis and other proliferative dermatoses is accumulation in the skin of the unusual arachidonic acid metabolite, 12R-hydroxyeicosatetraenoic acid (12R-HETE). This hydroxy fatty acid is opposite in chirality to the product of the well-known 12S-lipoxygenase and heretofore in mammals is known only as a product of cytochrome P450s. Here we provide mechanistic evidence for a lipoxygenase route to 12R-HETE in human psoriatic tissue and describe a 12R-lipoxygenase that can account for the biosynthesis. Initially we demonstrated retention of the C-12 deuterium of octadeuterated arachidonic acid in its conversion to 12R-HETE in incubations of psoriatic scales, indicating the end product is not formed by isomerization from 12S-H(P)ETE via the 12-keto derivative. Secondly, analysis of product formed from [10R-3H] and [10S-3H]-labeled arachidonic acids revealed that 12R-HETE synthesis is associated with stereospecific removal of the pro-R hydrogen from the 10-carbon of arachidonate. This result is compatible with 12R-lipoxygenase-catalyzed formation of 12R-HETE and not with a P450-catalyzed route to 12R-HETE in psoriatic scales. We cloned a lipoxygenase from human keratinocytes; the cDNA and deduced amino acid sequences share ≤50% identity to other human lipoxygenases. This enzyme, when expressed in Hela cells, oxygenates arachidonic acid to 12-HPETE, >98% 12R in configuration. The 12R-lipoxygenase cDNA is detectable by PCR in psoriatic scales and as a 2.5-kilobase mRNA by Northern analysis of keratinocytes. Identification of this enzyme extends the known distribution of R-lipoxygenases to humans and presents an additional target for potential therapeutic interventions in psoriasis.

Chiral molecular self-assembly of phospholipid tubules: A circular dichroism study

We report on spectroscopic studies of the chiral structure in phospholipid tubules formed in mixtures of alcohol and water. Synthetic phospholipids containing diacetylenic moieties in the acyl chains self-assemble into hollow, cylindrical tubules in appropriate conditions. Circular dichroism provides a direct measure of chirality of the molecular structure. We find that the CD spectra of tubules formed in mixtures of alcohol and water depends strongly on the alcohol used and the lipid concentration. The relative spectral intensity of different circular dichroism bands correlates with the number of bilayers observed using microscopy. The results provide experimental evidence that tubule formation is based on chiral packing of the lipid molecules and that interbilayer interactions are important to the tubule structure.

Symmetry arguments in chemistry

The use (and misuse) of symmetry arguments in constructing molecular models and in the interpretation of experimental observations bearing on molecular structure (spectroscopy, diffraction, etc.) is discussed. Examples include the development of point groups and space groups for describing the external and internal symmetry of crystals, the derivation of molecular symmetry by counting isomers (the benzene structure), molecular chirality, the connection between macroscopic and molecular chirality, pseudorotation, the symmetry group of nonrigid molecules, and the use of orbital symmetry arguments in discussing aspects of chemical reactivity.

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.