Self-assembly of trehalose molecules on a lysozyme surface: the broken glass hypothesis

To help understand how sugar interactions with proteins stabilise biomolecular structures, we compare the three main hypotheses for the phenomenon with the results of long molecular dynamics simulations on lysozyme in aqueous trehalose solution (0.75 M). We show that the water replacement and water entrapment hypotheses need not be mutually exclusive, because the trehalose molecules assemble in distinctive clusters on the surface of the protein. The flexibility of the protein backbone is reduced under the sugar patches supporting earlier findings that link reduced flexibility of the protein with its higher stability. The results explain the apparent contradiction between different experimental and theoretical results for trehalose effects on proteins.

Self-assembly of cross-linked β-cyclodextrin nanocapsules

Stirring of perthiolated β-cyclodextrin in water yields cross-linked hollow capsules ca. 50 nm in diameter, which can be used for encapsulation and controlled release of large molecules as shown using Reichardt's dye. © 2009 The Royal Society of Chemistry.

Condensation-enhanced self-assembly as a route to high surface area α-aluminas

High surface area nanosized α-alumina has been obtained by thermally treating a sol-gel-derived mesophase at 1200 C; the mesophase was synthesized by a sol-gel route involving evaporation induced self-assembly (EISA) of a hydrolyzed gel from Al-tri-sec-butoxide in s-BuOH in the presence of a nonionic surfactant (EO20PO70EO20), HCl as catalyst, and water (H2O/Al = 6). The activated material renders moderate surface areas of about 8.4-10 m2 g-1, associated with significant crystallite coarsening. The key aspect to produce smaller crystallites is making the mesophase more resistant to coarsening. This was achieved by enhancing the condensation step by treating the hydrolyzed gel with tetrabutyl ammonium hydroxide (TBAOH) before evaporation. The characteristics of the mesophase indicate condensation of the primary particles with less AlO5 unsaturated sites, at the expense of a lower solid yield due to small crystallites dissolution. The activated TBAOH condensed EISA material is composed of α-alumina aggregated crystallites of about 60-100 nm, and the material possesses surface areas ranging from 16 to 24 m2 g -1 due to the improved resistance to coarsening. At least two aspects are suggested to play a role in this. The worm-hole morphology of the mesophase aggregates yields high particle coordination, which favors densification rather than coarsening. Furthermore, the decrease of the AlO5 defect sites by the TBAOH condensation makes the mesophase less reactive and consequently more resistant to coarsening. © 2013 American Chemical Society.

Study of the kinetics and mechanism of rapid self-assembly in block copolymer thin films during solvo-microwave annealing

Microwave annealing is an emerging technique for achieving ordered patterns of block copolymer films on substrates. Little is understood about the mechanisms of microphase separation during the microwave annealing process and how it promotes the microphase separation of the blocks. Here, we use controlled power microwave irradiation in the presence of tetrahydrofuran (THF) solvent, to achieve lateral microphase separation in high- lamellar-forming poly(styrene-b-lactic acid) PS-b-PLA. A highly ordered line pattern was formed within seconds on silicon, germanium and silicon on insulator (SOI) substrates. In-situ temperature measurement of the silicon substrate coupled to condition changes during "solvo-microwave" annealing allowed understanding of the processes to be attained. Our results suggest that the substrate has little effect on the ordering process and is essentially microwave transparent but rather, it is direct heating of the polar THF molecules that causes microphase separation. It is postulated that the rapid interaction of THF with microwaves and the resultant temperature increase to 55 degrees C within seconds causes an increase of the vapor pressure of the solvent from 19.8 to 70 kPa. This enriched vapor environment increases the plasticity of both PS and PLA chains and leads to the fast self-assembly kinetics. Comparing the patterns formed on silicon, germanium and silicon on insulator (SOI) and also an in situ temperature measurement of silicon in the oven confirms the significance of the solvent over the role of substrate heating during "solvo-microwave" annealing. Besides the short annealing time which has technological importance, the coherence length is on a micron scale and dewetting is not observed after annealing. The etched pattern (PLA was removed by an Ar/O-2 reactive ion etch) was transferred to the underlying silicon substrate fabricating sub-20 nm silicon nanowires over large areas demonstrating that the morphology is consistent both across and through the film.

Fast assembly of fock matrices utilising symmetry properties of the basis set

A method of assembling the elements of the Fock matrix is described which is a modification of that due to Dacre. Lists of symmetry equivalent one-electron integrals are used as pointers to abbreviate the process of collecting two-electron integrals into the Fock matrix.

ENZYME-FREE UBIQUITIN LIGATION. FROM NATIVE CHEMICAL LIGATION AND SPIN LABELING TO DIMERIZATION BY INTER-UBIQUITIN MIMICKING LINKAGE AND PH-DEPENDENT CONFORMATIONAL SWITCH

The delicate balance between the production and disposal of proteins is vital for the changes required in the cell to respond to given stimulus. Ubiquitination is a protein modification with a range of signaling outcomes when ubiquitin is attached to a protein through a highly ordered enzymatic cascade process. Understanding ubiquitination is a growing field and nowadays the application of chemical reactions allows the isolation of quantitative materials for structural studies. Therefore, in this dissertation it is described some of these suitable chemical methodologies to produce an isopeptide bond toward the polymerization of ubiquitin bypassing the enzymatic control with the purpose of showing if these chemical modifications have a direct impact on the structure of ubiquitin. First, the possibility of incorporating non-natural lysine analogs known as mercaptolysines into the polypeptide chain of Ubiquitin was explored when they were attached to ubiquitin by native chemical ligation at its C terminus. The sulfhydryl group was used for the attachment of a paramagnetic label to map the surface of ubiquitin. Second, the condensation catalyzed by silver nitrate was used for the dimer assembly. In particular, the main focus was on examining whether orthogonal protection and deprotection of each monomer have an impact on the reaction yield, since the synthetic strategy has been previously attempted successfully. Third, the formation of ubiquitin dimers was approached by building an inter-ubiquitin linkage mimicking the isopeptide bond with two approaches, the classic disulfide exchange as well as the thiol-ene click reaction by thermal initiation in aqueous conditions. After assembling the dimeric units, they were studied by Nuclear Magnetic Resonance, in order to establish a conformational state profile which depends on the pH conditions. The latter is a very important concept since some ligands have a preferred affinity when the protein-protein hydrophobic patches are in close proximity.

Peripherally η1-Platinated Organometallic Porphyrins as Building Blocks for Multiporphyrin Arrays

The modification of peripherally metalated meso-η1-platiniometalloporphyrins, such as trans-[PtBr(NiDAPP)(PPh3)2] (H2DAPP = 5-phenyl-10,20-bis(3‘,5‘-di-tert-butylphenyl)porphyrin), leads to the analogous platinum(II) nitrato and triflato electrophiles in almost quantitative yields. Self-assembly reactions of these meso-platinioporphyrin tectons with pyridine, 4,4‘-bipyridine, or various meso-4-pyridylporphyrins in chloroform generate new multicomponent organometallic porphyrin arrays containing up to five porphyrin units. These new types of supramolecular arrays are formed exclusively in high yields and are stable in solution or in the solid state for extended periods. They were characterized by multinuclear NMR and UV−visible spectroscopy as well as high-resolution electrospray ionization mass spectrometry.

Sexual selection in a tropical fruit fly : role of a plant derived chemical in mate choice

The specific mechanisms by which selective pressures affect individuals are often difficult to resolve. In tephritid fruit flies, males respond strongly and positively to certain plant derived chemicals. Sexual selection by female choice has been hypothesized as the mechanism driving this behaviour in certain species, as females preferentially mate with males that have fed on these chemicals. This hypothesis is, to date, based on studies of only very few species and its generality is largely untested. We tested the hypothesis on different spatial scales (small cage and seminatural field-cage) using the monophagous fruit fly, Bactrocera cacuminata. This species is known to respond to methyl eugenol (ME), a chemical found in many plant species and one upon which previous studies have focused. Contrary to expectation, no obvious female choice was apparent in selecting ME-fed males over unfed males as measured by the number of matings achieved over time, copulation duration, or time of copulation initiation. However, the number of matings achieved by ME-fed males was significantly greater than unfed males 16 and 32 days after exposure to ME in small cages (but not in a field-cage). This delayed advantage suggests that ME may not influence the pheromone system of B. cacuminata but may have other consequences, acting on some other fitness consequence (e.g., enhancement of physiology or survival) of male exposure to these chemicals. We discuss the ecological and evolutionary implications of our findings to explore alternate hypotheses to explain the patterns of response of dacine fruit flies to specific plant-derived chemicals.

Growth of boehmite nanofibers by assembling nanoparticles with surfactant micelles

It is known that boehmite (AlOOH) nanofibers formed in the presence of nonionic poly(ethylene oxide) (PEO) surfactant at 373 K. A novel approach is proposed in this study for the growth of the boehmite nanofibers: when fresh aluminum hydrate precipitate was added at regular interval to initial mixture of boehmite and PEO surfactant at 373 K, the nanofibers grow from 40 to 50 nm long to over 100 nm. It is believed that the surfactant micelles play an important role in the nanofiber growth: directing the assembly of aluminum hydrate particles through hydrogen bonding with the hydroxyls on the surface of aluminum hydrate particles. Meanwhile a gradual improvement in the crystallinity of the fibers during growth is observed and attributed to the Ostwald ripening process. This approach allows us to precisely control the size and morphology of boehmite nanofibers using soft chemical methods and could be useful for low temperature, aqueous syntheses of other oxide nanomaterials with tailorable structural specificity such as size, dimension and morphology.