Synthesis and immunological characterization of 104-mer and 102-mer peptides corresponding to the N- and C-terminal regions of the Plasmodium falciparum CS protein.

We investigated the immunogenicity and the conformational properties of the non-repetitive sequences of the Plasmodium falciparum circumsporozoite (CS) protein. Two polypeptides of 104 and 102 amino acids long, covering, respectively, the N- and C-terminal regions of the CS protein, were synthesized using solid phase Fmoc chemistry. The crude polypeptides were purified by a combination of size exclusion chromatography and RP-HPLC. Sera of mice immunized with the free polypeptides emulsified in incomplete Freund's adjuvant strongly reacted with the synthetic polypeptides as well as with native CS protein as judged by ELISA and IFAT assays. Most importantly, these antisera inhibited the sporozoite invasion of hepatoma cells. In addition, sera derived from donors living in a malaria endemic area recognized the CS 104- and 102-mers. Conformational studies of the CS polypeptides were also performed by circular dichroism spectroscopy showing the presence of a weakly ordered structure that can be increased by addition of trifluoroethanol. The obtained results indicate that the synthetic CS polypeptides and the natural CS protein share some common antigenic determinants and probably have similar conformation. The approach used in this study might be useful for the development of a synthetic malaria vaccine.

Aminoterminal amphipathic α-helix AH1 of hepatitis C virus nonstructural protein 4B possesses a dual role in RNA replication and virus production.

Nonstructural protein 4B (NS4B) is a key organizer of hepatitis C virus (HCV) replication complex formation. In concert with other nonstructural proteins, it induces a specific membrane rearrangement, designated as membranous web, which serves as a scaffold for the HCV replicase. The N-terminal part of NS4B comprises a predicted and a structurally resolved amphipathic α-helix, designated as AH1 and AH2, respectively. Here, we report a detailed structure-function analysis of NS4B AH1. Circular dichroism and nuclear magnetic resonance structural analyses revealed that AH1 folds into an amphipathic α-helix extending from NS4B amino acid 4 to 32, with positively charged residues flanking the helix. These residues are conserved among hepaciviruses. Mutagenesis and selection of pseudorevertants revealed an important role of these residues in RNA replication by affecting the biogenesis of double-membrane vesicles making up the membranous web. Moreover, alanine substitution of conserved acidic residues on the hydrophilic side of the helix reduced infectivity without significantly affecting RNA replication, indicating that AH1 is also involved in virus production. Selective membrane permeabilization and immunofluorescence microscopy analyses of a functional replicon harboring an epitope tag between NS4B AH1 and AH2 revealed a dual membrane topology of the N-terminal part of NS4B during HCV RNA replication. Luminal translocation was unaffected by the mutations introduced into AH1, but was abrogated by mutations introduced into AH2. In conclusion, our study reports the three-dimensional structure of AH1 from HCV NS4B, and highlights the importance of positively charged amino acid residues flanking this amphipathic α-helix in membranous web formation and RNA replication. In addition, we demonstrate that AH1 possesses a dual role in RNA replication and virus production, potentially governed by different topologies of the N-terminal part of NS4B.

Direct Observation of Magnetic Metastability in Individual Iron Nanoparticles

X-ray photoemission electron microscopy combined with x-ray magnetic circular dichroism is used to study the magnetic properties of individual iron nanoparticles with sizes ranging from 20 down to 8 nm. While the magnetocrystalline anisotropy of bulk iron suggests superparamagnetic behavior in this size range, ferromagnetically blocked particles are also found at all sizes. Spontaneous transitions from the blocked state to the superparamagnetic state are observed in single particles and suggest that the enhanced magnetic energy barriers in the ferromagnetic particles are due to metastable, structurally excited states with unexpected life times

Direct Observation of Magnetic Metastability in Individual Iron Nanoparticles

X-ray photoemission electron microscopy combined with x-ray magnetic circular dichroism is used to study the magnetic properties of individual iron nanoparticles with sizes ranging from 20 down to 8 nm. While the magnetocrystalline anisotropy of bulk iron suggests superparamagnetic behavior in this size range, ferromagnetically blocked particles are also found at all sizes. Spontaneous transitions from the blocked state to the superparamagnetic state are observed in single particles and suggest that the enhanced magnetic energy barriers in the ferromagnetic particles are due to metastable, structurally excited states with unexpected life times

Bonding of gold nanoclusters to oxygen vacancies on rutile TiO2(110)

Through an interplay between scanning tunneling microscopy (STM) and density functional theory (DFT) calculations, we show that bridging oxygen vacancies are the active nucleation sites for Au clusters on the rutile TiO2(110) surface. We find that a direct correlation exists between a decrease in density of vacancies and the amount of Au deposited. From the DFT calculations we find that the oxygen vacancy is indeed the strongest Au binding site. We show both experimentally and theoretically that a single oxygen vacancy can bind 3 Au atoms on average. In view of the presented results, a new growth model for the TiO2(110) system involving vacancy-cluster complex diffusion is presented.

Growth and magnetic characterization of Co nanoparticles obtained by femtosecond pulsed laser deposition.

We present a detailed study on the morphology and magnetic properties of Co nanostructures deposited onto oxidized Si substrates by femtosecond pulsed laser deposition. Generally, Co disks of nanometric dimensions are obtained just above the ablation threshold, with a size distribution characterized by an increasingly larger number of disks as their size diminishes, and with a maximum disk size that depends on the laser power density. In Au/Co/Au structures, in-plane magnetic anisotropy is observed in all cases, with no indication of superparamagnetism regardless of the amount of material or the laser power density. Magnetic force microscopy observations show coexistence of single-domain and vortex states for the magnetic domain structure of the disks. Superconducting quantum interference device magnetometry and x-ray magnetic circular dichroism measurements point to saturation magnetization values lower than the bulk, probably due to partial oxidation of the Co resulting from incomplete coverage by the Au capping layer.

Gas-phase solvolysis type reactions of SiCl3+ cations

Gas-phase SiCl3+ ions undergo sequential solvolysis type reactions with water, methanol, ammonia, methylamine and propylene. Studies carried out in a Fourier Transform mass spectrometer reveal that these reactions are facile at 10-8 Torr and give rise to substituted chlorosilyl cations. Ab initio and DFT calculations reveal that these reactions proceed by addition of the silyl cation to the oxygen or nitrogen lone pair followed by a 1,3-H migration in the transition state. These transition states are calculated to lie below the energy of the reactants. By comparison, hydrolysis of gaseous CCl3+ is calculated to involve a substantial positive energy barrier.

Interação de átomos leves com clusters de metais de transição

Density Functional Theory (DFT) calculations on the interactions of small atoms (H, C, O, and S) on first-row transition metal clusters were performed. The results show that the adsorption site may vary between the metal surface and the edge of the cluster. The adsorption energies, adatom-nearest neighbor and adatom-metal plane distances were also determined. Finally, the authors present a discussion about the performance of these metals as anodes on solid oxide fuel cells. The results obtained agree with empirical data, indicating that the theoretical model used is adequate

Rotenoids from Tephrosia toxicaria with larvicidal activity against Aedes aegypti, the main vector of dengue fever

In the search for new larvicides from plants, we have investigated the potential activity of the rotenoids deguelin (1), 12a-hydroxy-α-toxicarol (2) and tephrosin (3), isolated from the bioactive ethanol extract of roots of Tephrosia toxicaria Pers., against Aedes aegypti, the main vector of dengue. The absolute configuration of these compounds was determined by circular dichroism (CD) spectra. The LC50 values of the compounds evaluated justify the potential of T. toxicaria as a new natural larvicide.

Descriptores globales y locales de la reactividad para el diseño de nuevos fármacos anticancerosos basados en cis-platino(II)

Density functional theory was used to investigate the global and local reactivity of some cis-platinum(II) complexes including anticancer drugs, such as cisplatin and carboplatin. Calculated equilibrium geometries at mPW1PW/LANL2DZ* are in close agreement with their available X-ray data. We develop three new local reactivity descriptors: atomic descriptor of philicity, atomic descriptor group and atomic descriptor of philicity group for determining chemical reactivity and selectivity of the studied complexes. This contribution on chemical reactivity allow us to establish qualitative trends, which enable our descriptors for use in rational platinum based anticancer drug design.

Effect of triplet encapsulated atoms in [60] fullerenes: a theoretical analysis

The present investigation reports on the interaction of the C/O triplet atoms inside of the [60] fullerene (C60) species with small polar molecules (H²O, CH³OH, HF, NH³) using Density Functional Theory (DFT) calculations. The calculations show that in all the computed cases the encapuslated complexes with the molecules are more stable than without internal atoms.

Defects in Persistent Luminescence Materials

Persistent luminescence materials can store energy from solar radiation or artificial lighting and release it over a period of several hours without a continuous excitation source. These materials are widely used to improve human safety in emergency and traffic signalization. They can also be utilized in novel applications including solar cells, medical diagnostics, radiation detectors and structural damage sensors. The development of these materials is currently based on methods based on trial and error. The tailoring of new materials is also hindered by the lack of knowledge on the role of their intrinsic and extrinsic lattice defects in the appropriate mechanisms. The goal of this work was to clarify the persistent luminescence mechanisms by combining ab initio density functional theory (DFT) calculations with selected experimental methods. The DFT approach enables a full control of both the nature of the defects and their locations in the host lattice. The materials studied in the present work, the distrontium magnesium disilicate (Sr₂MgSi₂O₇) and strontium aluminate (SrAl₂O₄) are among the most efficient persistent luminescence hosts when doped with divalent europium Eu²⁺ and co-doped with trivalent rare earth ions R³⁺ (R: Y, La-Nd, Sm, Gd-Lu). The polycrystalline materials were prepared with the solid state method and their structural and phase purity was confirmed by X-ray powder diffraction. Their local crystal structure was studied by high-resolution transmission electron microscopy. The crystal and electronic structure of the nondoped as well as Eu²⁺, R^2+/3+ and other defect containing materials were studied using DFT calculations. The experimental trap depths were obtained using thermoluminescence (TL) spectroscopy. The emission and excitation of Sr₂MgSi₂O₇:Eu²+,Dy³⁺ were also studied. Significant modifications in the local crystal structure due to the Eu²⁺ ion and lattice defects were found by the experimental and DFT methods. The charge compensation effects induced by the R³⁺ co-doping further increased the number of defects and distortions in the host lattice. As for the electronic structure of Sr₂MgSi₂O₇ and SrAl₂O₄, the experimental band gap energy of the host materials was well reproduced by the calculations. The DFT calculated Eu²⁺ and R^2+/3+ 4fn as well as 4f^n-15d¹ ground states in the Sr₂MgSi₂O₇ band structure provide an independent verification for an empirical model which is constructed using rather sparse experimental data for the R³⁺ and especially the R²⁺ ions. The intrinsic and defect induced electron traps were found to act together as energy storage sites contributing to the materials’ efficient persistent luminescence. The calculated trap energy range agreed with the trap structure of Sr₂MgSi₂O₇ obtained using TL measurements. More experimental studies should be carried out for SrAl₂O₄ to compare with the DFT calculations. The calculated and experimental results show that the electron traps created by both the rare earth ions and vacancies are modified due to the defect aggregation and charge compensation effects. The relationships between this modification and the energy storage properties of the solid state materials are discussed.

Research and development of III-V semiconductor surfaces for improved device interfaces

This thesis is devoted to understanding and improving technologically important III-V compound semiconductor (e.g. GaAs, InAs, and InSb) surfaces and interfaces for devices. The surfaces and interfaces of crystalline III-V materials have a crucial role in the operation of field-effect-transistors (FET) and highefficiency solar-cells, for instance. However, the surfaces are also the most defective part of the semiconductor material and it is essential to decrease the amount of harmful surface or interface defects for the next-generation III-V semiconductor device applications. Any improvement in the crystal ordering at the semiconductor surface reduces the amount of defects and increases the material homogeneity. This is becoming more and more important when the semiconductor device structures decrease to atomic-scale dimensions. Toward that target, the effects of different adsorbates (i.e., Sn, In, and O) on the III-V surface structures and properties have been investigated in this work. Furthermore, novel thin-films have been synthesized, which show beneficial properties regarding the passivation of the reactive III-V surfaces. The work comprises ultra-high-vacuum (UHV) environment for the controlled fabrication of atomically ordered III-V(100) surfaces. The surface sensitive experimental methods [low energy electron diffraction (LEED), scanning tunneling microscopy/spectroscopy (STM/STS), and synchrotron radiation photoelectron spectroscopy (SRPES)] and computational density-functionaltheory (DFT) calculations are utilized for elucidating the atomic and electronic properties of the crucial III-V surfaces. The basic research results are also transferred to actual device tests by fabricating metal-oxide-semiconductor capacitors and utilizing the interface sensitive measurement techniques [capacitance voltage (CV) profiling, and photoluminescence (PL) spectroscopy] for the characterization. This part of the thesis includes the instrumentation of home-made UHV-compatible atomic-layer-deposition (ALD) reactor for growing good quality insulator layers. The results of this thesis elucidate the atomic structures of technologically promising Sn- and In-stabilized III-V compound semiconductor surfaces. It is shown that the Sn adsorbate induces an atomic structure with (1×2)/(1×4) surface symmetry which is characterized by Sn-group III dimers. Furthermore, the stability of peculiar ζa structure is demonstrated for the GaAs(100)-In surface. The beneficial effects of these surface structures regarding the crucial III-V oxide interface are demonstrated. Namely, it is found that it is possible to passivate the III-V surface by a careful atomic-scale engineering of the III-V surface prior to the gate-dielectric deposition. The thin (1×2)/(1×4)-Sn layer is found to catalyze the removal of harmful amorphous III-V oxides. Also, novel crystalline III-V-oxide structures are synthesized and it is shown that these structures improve the device characteristics. The finding of crystalline oxide structures is exploited by solving the atomic structure of InSb(100)(1×2) and elucidating the electronic structure of oxidized InSb(100) for the first time.

Partially folded intermediates during trypsinogen denaturation

The equilibrium unfolding of bovine trypsinogen was studied by circular dichroism, differential spectra and size exclusion HPLC. The change in free energy of denaturation was = 6.99 ± 1.40 kcal/mol for guanidine hydrochloride and = 6.37 ± 0.57 kcal/mol for urea. Satisfactory fits of equilibrium unfolding transitions required a three-state model involving an intermediate in addition to the native and unfolded forms. Size exclusion HPLC allowed the detection of an intermediate population of trypsinogen whose Stokes radii varied from 24.1 ± 0.4 Å to 26.0 ± 0.3 Å for 1.5 M and 2.5 M guanidine hydrochloride, respectively. During urea denaturation, the range of Stokes radii varied from 23.9 ± 0.3 Å to 25.7 ± 0.6 Å for 4.0 M and 6.0 M urea, respectively. Maximal intrinsic fluorescence was observed at about 3.8 M urea with 8-aniline-1-naphthalene sulfonate (ANS) binding. These experimental data indicate that the unfolding of bovine trypsinogen is not a simple transition and suggest that the equilibrium intermediate population comprises one intermediate that may be characterized as a molten globule. To obtain further insight by studying intermediates representing different stages of unfolding, we hope to gain a better understanding of the complex interrelations between protein conformation and energetics.

Effects of 60Co gamma radiation on crotamine

Ionizing radiation can change the molecular structure and affect the biological properties of biomolecules. This has been employed to attenuate animal toxins. Crotamine is a strongly basic polypeptide (pI 10.3) from Crotalus durissus terrificus venom composed of 42 amino acid residues. It induces skeletal muscle spasms leading to a spastic paralysis of hind limbs in mice. The objective of the present study was to carry out a biochemical study and a toxic activity assay on native and irradiated crotamine. Crotamine was purified from C.d. terrificus venom by Sephadex G-100 gel filtration followed by ion-exchange chromatography, and irradiated at 2 mg/ml in 0.15 M NaCl with 2.0 kGy gamma radiation emitted by a 60Co source. The native and irradiated toxins were evaluated in terms of structure and toxic activity (LD50). Irradiation did not change the protein concentration, the electrophoretic profile or the primary structure of the protein although differences were shown by spectroscopic techniques. Gamma radiation reduced crotamine toxicity by 48.3%, but did not eliminate it.