Ubiquitous deprotonation of terephthalic acid in the self-assembled phases on Cu(100).

We performed an exhaustive study of terephthalic acid (TPA) self-assembly on a Cu(100) surface, where first-layer molecules display two sequential phase transitions in the 200-400 K temperature range, corresponding to different stages of molecular deprotonation. We followed the chemical and structural changes by means of high-resolution X-ray photoelectron spectroscopy (XPS) and variable-temperature scanning tunneling microscopy (STM), which were interpreted on the basis of density functional theory (DFT) calculations and photoemission simulations. In order to reveal the spectroscopic contributions of the molecules in different states of deprotonation, we modified the substrate reactivity by deposition of a small amount of Sn, which hampers the deprotonation reaction. We found that the characteristic molecular ribbons of the TPA/Cu(100) α-phase at a low temperature contain a significant fraction of partially deprotonated molecules, in contrast to the expectation of a fully protonated phase, where the self-assembly was claimed to be simply driven by the intermolecular double hydrogen bonds [OHO]. On the basis of our simulations, we propose a model where the carboxylate groups of the partially deprotonated molecules form single hydrogen bonds with the carboxylic groups of the fully protonated molecules. Using real time XPS, we also monitored the kinetics of the deprotonation reaction. We show that the network of mixed single and double hydrogen bonds inhibits further deprotonation up to ∼270 K, whereas the isolated molecules display a much lower deprotonation barrier.

Tuning the catalytic activity of Ag(110)-supported Fe phthalocyanine in the oxygen reduction reaction.

A careful choice of the surface coverage of iron phthalocyanine (FePc) on Ag (110) around the single monolayer allows us to drive with high precision both the long-range supramolecular arrangement and the local adsorption geometry of FePc molecules on the given surface. We show that this opens up the possibility of sharply switching the catalytic activity of FePc in the oxygen reduction reaction and contextual surface oxidation in a reproducible way. A comprehensive and detailed picture built on diverse experimental evidence from scanning tunnelling microscopy, X-ray photoelectron spectroscopy and X-ray absorption spectroscopy, coupled with density functional theory calculations, sheds new light on the nature of the catalytically active molecule-surface coordination and on the boundary conditions for its occurrence. The results are of relevance for the improvement of the catalytic efficiency of metallo-macrocycles as viable substitutes for platinum in the cathodic compartment of low-temperature fuel cells.

Intrinsic nature of the excess electron distribution at the TiO2(110) surface.

The gap state that appears upon reduction of TiO2 plays a key role in many of titania's interesting properties but its origin and spatial localization have remained unclear. In the present work, the TiO2(110) surface is reduced in a chemically controlled way by sodium adsorption. By means of resonant photoelectron diffraction, excess electrons are shown to be distributed mainly on subsurface Ti sites strikingly similar to the defective TiO2(110) surface, while any significant contribution from interstitial Ti ions is discarded. In agreement with first principles calculations, these findings demonstrate that the distribution of the band gap charge is an intrinsic property of TiO2(110), independent of the way excess electrons are produced.

Functional K-doping of eumelanin thin films: Density functional theory and soft x-ray spectroscopy experiments in the frame of the macrocyclic protomolecule model [corrected].

We demonstrate the possibility to achieve the doping of eumelanin thin films through K(+) incorporation during the electrodeposition of the film. K-doping changes the optical properties of the eumelanin thin films, reducing the energy gap from 1.0 to 0.6 eV, with possible implications for the photophysical properties. We have identified the doping-related occupied and unoccupied electronic states and their spectral weight using resonant photoemission spectroscopy (ResPES) and x-ray absorption at the C and N K-edges (near edge x-ray absorption fine spectroscopy, NEXAFS). All data are consistently interpreted by ab initio calculations of the electronic structure within the frame of the macrocycle model developed for the eumelanin protomolecule. Our analysis puts in evidence the intercalation of K with one specific oligomer (a tetramer composed of one indolequinone and 3 hydroquinone monomers) in correspondence of the nitrogen macrocycle. The predicted variation of the tetramer spacing is also in agreement with the recent x-ray diffraction experiments. The charge donation from K to N and C atoms gives rise to new electronic states at the top of the valence band and in NEXAFS resonances of the unoccupied orbitals. The saturation of the tetramer macrocycles leaves an excess of K that bind to N and C atoms in alternative configurations, as witnessed by the occurrence of additional spectral features in the carbon-related ResPES measurements.

Relating energy level alignment and amine-linked single molecule junction conductance.

Using photoemission spectroscopy, we determine the relationship between electronic energy level alignment at a metal-molecule interface and single-molecule junction transport data. We measure the position of the highest occupied molecular orbital (HOMO) relative to the Au metal Fermi level for three 1,4-benzenediamine derivatives on Au(111) and Au(110) with ultraviolet and resonant X-ray photoemission spectroscopy. We compare these results to scanning tunnelling microscope-based break-junction measurements of single molecule conductance and to first-principles calculations. We find that the energy difference between the HOMO and Fermi level for the three molecules adsorbed on Au(111) correlate well with changes in conductance and agree well with quasiparticle energies computed from first-principles calculations incorporating self-energy corrections. On the Au(110) that presents Au atoms with lower-coordination, critical in break-junction conductance measurements, we see that the HOMO level shifts further from the Fermi level. These results provide the first direct comparison of spectroscopic energy level alignment measurements with single molecule junction transport data.

De novo design of fibrils made of short alpha-helical coiled coil peptides.

BACKGROUND: The alpha-helical coiled coil structures formed by 25-50 residues long peptides are recognized as one of Nature's favorite ways of creating an oligomerization motif. Known de novo designed and natural coiled coils use the lateral dimension for oligomerization but not the axial one. Previous attempts to design alpha-helical peptides with a potential for axial growth led to fibrous aggregates which have an unexpectedly big and irregular thickness. These facts encouraged us to design a coiled coil peptide which self-assembles into soluble oligomers with a fixed lateral dimension and whose alpha-helices associate in a staggered manner and trigger axial growth of the coiled coil. Designing the coiled coil with a large number of subunits, we also pursue the practical goal of obtaining a valuable scaffold for the construction of multivalent fusion proteins. RESULTS: The designed 34-residue peptide self-assembles into long fibrils at slightly acid pH and into spherical aggregates at neutral pH. The fibrillogenesis is completely reversible upon pH change. The fibrils were characterized using circular dichroism spectroscopy, sedimentation diffusion, electron microscopy, differential scanning calorimetry and X-ray fiber diffraction. The peptide was deliberately engineered to adopt the structure of a five-stranded coiled coil rope with adjacent alpha-helices, staggered along the fibril axis. As shown experimentally, the most likely structure matches the predicted five-stranded arrangement. CONCLUSIONS: The fact that the peptide assembles in an expected fibril arrangement demonstrates the credibility of our conception of design. The discovery of a short peptide with fibril-forming ability and stimulus-sensitive behavior opens new opportunities for a number of applications.

Characterization of murine monoclonal antibodies against a repetitive synthetic peptide from the circumsporozoite protein of the human malaria parasite, Plasmodium falciparum.

Monoclonal antibodies (mAbs) were raised in mice against the synthetic peptide (NANP)40, consisting of 40 (NANP) repeats of the circumsporozoite (CS) protein of the human malaria parasite, Plasmodium falciparum, and characterized. (i) Five of these mAbs recognized the P. falciparum CS protein in western blot experiments and in immunofluorescence assays using different preparations of sporozoites. The remaining two mAbs (CT3.2 and CT3.3, both IgG1) gave negative results by both techniques. (ii) When the anti-(NANP)40 peptide mAbs were functionally tested in vitro to assess their ability to inhibit the attachment and penetration of the parasites into cultured human liver cells, six of them exhibited inhibitory activities ranging between 66 and 90%. CT3.2 mAbs, also, inhibited sporozoite attachment and penetration, despite the negative results by immunofluorescence and western blot experiments. However, when immunofluorescence was repeated in the presence of calcium, CT3.2 did reveal a positive recognition of P. falciparum sporozoites, suggesting that this mAb could recognize the (NANP) sequence when calcium was bound to the repetitive peptide. (iii) Furthermore, the binding of an anti-(NANP)40 IgM mAb (CT1) to the solid-phase peptide was not inhibited by preincubation of the peptide with a mAb against the P. falciparum CS protein. (iv) Finally, one anti-(NANP)40 IgG1 mAb (CT3.1) was unable to bind to the shorter (NANP)3 peptide, although it recognized the (NANP)40 peptide and the P. falciparum CS protein. The results presented here suggest that heterogeneous antibody populations are produced upon immunization of mice with (NANP)40 synthetic peptide and that epitopes different from those simply related to the linear (NANP) amino acid sequence are likely to be present in long (NANP)n constructs as well as in the repetitive domain of the P. falciparum CS protein.

Immunostimulation by a partially modified retro-inverso-tuftsin analogue containing Thr1 psi[NHCO](R,S)Lys2 modification.

The tuftsin retro-inverso analogue H-Thr psi[NHCO](R,S)Lys-Pro-Arg-OH was synthesized through a novel procedure for the high-yield incorporation of isolated retro-inverso bonds into peptide chains and the use of the new Meldrum's acid derivative (CH3)2C(OCO)2CH(CH2)4NHCOCF3 followed by its efficient coupling in solution to trimethylsilylated H-D-Thr(t-Bu)NH2. Closely related peptide impurities were eliminated both from the crude final peptide and the fully protected tetrapeptide amide precursor via ion-exchange and reversed-phase displacement chromatography, respectively. The tuftsin retro-inverso analogue proved to be completely resistant to enzymatic degradation in vitro, either against isolated aminopeptidases or human plasma proteolytic enzymes. When administered either orally or intravenously, it was significantly more active than normal tuftsin in increasing the number of specific antibody secreting cells in spleen of mice immunized with sheep erythrocytes. Furthermore, the analogue exerted an enhanced stimulatory effect on the cytotoxic activity of splenocytes against YAC-1 tumor cells. Finally, retro-inverso-tuftsin was about 10-fold more potent than the native peptide in reducing rat adjuvant arthritis. The resistance of the retro-inverso analogue to peptidases might explain the increased in vivo activities and allows its further immunopharmacological characterization.

Natural antibodies against three distinct and defined antigens of Plasmodium falciparum in residents of a mesoendemic area in Gabon.

The magnitude of the antibody response to three distinct and defined antigens of Plasmodium falciparum was assessed in 144 inhabitants of the Kassa district (Haut Ogooué Province, Gabon), a region where malaria is mesoendemic. Antibodies against a polypeptide consisting of 40 (Asn-Ala-Asn-Pro) repeats of P. falciparum circumsporozoite protein [(NANP)40] were detected by ELISA. Antibodies against the fusion peptide 31.1, which consists of the N-terminal portion of the 190-200 kDa glycoprotein, were also detected by ELISA. Antibodies against ring-infected erythrocyte surface antigens (RESA), mainly the P. falciparum 155 kDa antigen (Pf 155), were detected by IFA on glutaraldehyde-fixed P. falciparum infected red blood cells (IRBC). In addition, a standard IFA employing air-dried P. falciparum IRBC was used to detect antibodies against intraerythrocytic asexual forms. Parasitemia and spleen enlargement were also recorded. The frequency of sera positive for specific antibodies increased with age for all the antigens tested. Plateau antibody levels were reached at different ages for the different antigens. Individual antibody responses varied in titer to the different antigens. Subjects with parasite-negative thick smears showed higher titers of anti-31.1 as well as an increased frequency of anti-RESA antibodies compared to subjects having positive smears. No differences in the titer and in the prevalence of anti-(NANP)40 antibodies were found between these groups. The results suggest that the antibody response against asexual blood stage antigens, especially anti-RESA and anti-31.1, may play a role in controlling parasitemia.

Use of synthetic peptides in the study of the antibody response to Plasmodium vivax sporozoites.

Synthetic peptides reproducing 4 DRADGQPAG (D4) and a sequential array of DRADGQPAG and DRAAGQPAG repeats (DDAAD) of the Plasmodium vivax circumsporozoite (CS) protein were investigated for their potential use in the detection of P. vivax sporozoite antibodies in human sera. These peptides specifically inhibited the binding of monoclonal antibodies to the P. vivax CS protein in Western blots. However, when D4 and DDAAD peptides were used in an enzyme-linked immunosorbent assay (ELISA) for the detection of human antibodies, more sera bound to the DDAAD (61%) than to the D4 peptide (22%). This binding was specific, and suggested that the DDAAD peptide contained epitopes constituted by the sequential array of DRADGQPAG and DRAAGQPAG repeat variants and absent in the D4 peptide. The ELISA using the DDAAD peptide was applied to the detection of P. vivax CS protein antibodies in a large number of sera from Kataragama, an endemic area in Sri Lanka. The prevalence of these antibodies increased with age, reaching 40% in adults greater than 50 years old. The ELISA employing the DDAAD peptide represents a simple and useful tool for the analysis of the antibody response to P. vivax sporozoites in naturally exposed individuals.

Antibodies to the repetitive epitope of Plasmodium falciparum circumsporozoite protein in a rural Tanzanian community: a longitudinal study of 132 children.

An ELISA employing a novel synthetic peptide consisting of 40 (Asn-Ala-Asn-Pro) repeats of Plasmodium falciparum circumsporozoite protein, (NANP)40, was used to detect antibodies against P. falciparum circumsporozoite protein in 132 children, 1 month to 15 years old, from a rural community (Kikwawila village) of Tanzania, a region where malaria is hyperendemic. The children were surveyed comprehensively over 3 consecutive years for clinical, parasitological, and serological parameters. Entomological data were also gathered for selected households in this village. The following results were obtained: anti-(NANP)40 antibodies increased as a function of age; the majority of children over 10 years showed a stable positivity for such antibodies during the longitudinal study; a negative correlation was observed between the levels of anti-sporozoite antibodies and both spleen enlargement and the presence of parasites in thick smears; no relationship was found between anti-(NANP)40 antibodies and asexual blood stage antibodies; children living in two representative households with comparable indoor resting mosquito densities showed markedly different frequencies of anti-(NANP)40 antibodies, in spite of comparable clinical, parasitological, and serological parameters. Thus, in addition to the exposure to infectious mosquito bites, other (e.g., genetic) factors, may play a role in the ability of certain individuals to mount an antibody response against this immunodominant repetitive epitope. The results presented in this paper confirm that the (NANP)40-ELISA represents a simple, reliable means for the detection of anti-(NANP)40 circumsporozoite protein antibodies and suggest that such antibodies may contribute to the immune protection against malaria in humans.

Antibodies to Plasmodium falciparum sporozoites following a malarial outbreak in a non-endemic area of Sri Lanka.

An enzyme-linked immunosorbent assay (ELISA) based on the synthetic peptide (NANP)40 was used to characterize the sporozoite antibodies in an unusual Plasmodium falciparum outbreak in a non-malarious area in Sri Lanka. A positive antibody response was seen in 62% of patients with their first P. falciparum illness. There was no correlation between sporozoite antibodies and the antibody against blood stages, determined by immunofluorescence assay. The majority (91%) of the patients lost the antibodies to circumsporozoite (CS) protein within one year (in the absence of re-exposure). Three patients had high levels of CS antibodies even after one year, and this persistence was related to the level of the initial antibody response. In the area of the outbreak 10% of schoolchildren had antibodies to the (NANP)40 peptide. 21% of the 42 children with present or past overt malaria were antibody positive. Of the children with no such background, 8% were antibody positive. The corresponding seropositivity rates for asexual blood stages were 31% and 1% for the 2 groups respectively. It is concluded that (NANP)40 ELISA is potentially a valuable tool in sero-epidemiology, particularly in situations of seasonal transmission and recurrences due to drug resistance.

Age-related prevalence of antibody response against three different, defined Plasmodium falciparum antigens in children from the Haut-Ogooué province in Gabon.

The kinetics of the humoral response to defined Plasmodium falciparum antigens was studied in 543 children, 1 month to 15 years old, living in an area endemic for malaria. The antigens used for enzyme-linked immunosorbent assay were (i) the synthetic peptide (NANP)40 representing the immunodominant repeated region of the circumsporozoite protein, and (ii) the fusion peptide 31.1, representing the N-terminal portion of the 83 kDa polypeptide expressed at the surface of merozoites which is a processed product of the 190-200 kDa glycoprotein. In addition, glutaraldehyde-fixed infected red blood cells (RBC) were used to detect ring-infected erythrocyte surface antigen (RESA) and unfixed infected RBC to detect intra-erythrocytic asexual form (IEF) antigens by immunofluorescence. In the 1 to 2 months age group, 50%, 26% and 21% of the children had antibodies for IEF, (NANP)40 and 31.1 respectively, but none had anti-RESA antibodies. The proportions of positive subjects decreased until 3 to 6 months and then increased progressively for the 4 antigens, approaching, but not reaching, adult values by the age of 15 years. Antibodies against specific antigens were acquired concomitantly. Children born from (NANP)40-positive mothers showed enhanced anti-(NANP)40 IgG responses.

Poly(DL-proline), a synthetic polypeptide behaving as an ion channel across bilayer membranes.

The synthesis and characterization of poly(DL-proline) are reported in relation with its predicted property of forming ion channels across membranes. The analysis of the conductance induced in synthetic bilayer membranes doped with poly(DL-proline) shows ionic permeoselectivity and the characteristic time course of fluctuations of ion channels, according to the similarity with the active structure of gramicidin A in membranes during the ion passage. An alternative mechanism of ion transport across bilayer membranes is also advanced.

Detection of antibodies to Plasmodium falciparum sporozoites by employing synthetic peptides.

A new achievement in the immunodiagnosis of malaria has been reached after the knowledge of the molecular structure of some plasmodial antigens has become available. One example is given by the repetitive immunodominant epitope of Plasmodium falciparum circumsporozoite protein, which consists of 4 tandemly repeated aminoacids (Asn-Ala-Asn-Pro = NANP). A large synthetic peptide reproducing 40 NANP repeats, (NANP)40, has been shown to reproduce efficiently the native antigen in the CS protein and has been used to develop an enzyme-linked immunosorbent assay (ELISA) for the detection of antisporozoite antibodies in individuals from malaria-endemic countries. This (NANP)40 ELISA has been employed in a longitudinal study in a rural community in Tanzania. The results obtained have shown (i) that the presence of anti-(NANP) antibodies is associated with a certain degree of protective immunity; and (ii) that genetic factors could play a role in the host immune responsiveness to (NANP). Such an ELISA can be easily applied to field research and can be useful for monitoring the immune status of populations participating, in the future, to malaria vaccination trials employing P. falciparum sporozoite peptides.

Tracking the excitation dynamics in the Mn:Ge(111) metallic interface by resonant electron spectroscopy.

Resonant photoemission from the valence band of a (√3 × âˆš3)R30° reconstructed Mn:Ge(111) metallic interface has been carefully analyzed with the aim to track the transition from resonant Raman to normal Auger emission. The transition energy has been compared with the Mn 2p binding energy, as well as with the Mn L(3) absorption edge energy. Close similarities emerge with respect to the case of elemental Mn thin films, suggesting that the excitation dynamics is dominated by the electronic properties of Mn 3d states, in spite of the bonding with Ge atoms. The switching from the resonant Raman Auger (RRAS) to the normal Auger regime is found about 2 eV below the Mn L(3) absorption edge. A change of the lineshape due to the transition from an overall N - 1 electron final state (RRAS channel) to an N - 2 electron final state (normal Auger channel) is evidenced by the analysis of the experimental data, which also allowed the ratio to be tracked between charge delocalization and core-hole time scales as the photon energy is tuned across the Mn L(3) edge.

X-ray diffraction and computation yield the structure of alkanethiols on gold(111).

The structure of self-assembled monolayers (SAMs) of long-chain alkyl sulfides on gold(111) has been resolved by density functional theory-based molecular dynamics simulations and grazing incidence x-ray diffraction for hexanethiol and methylthiol. The analysis of molecular dynamics trajectories and the relative energies of possible SAM structures suggest a competition between SAM ordering, driven by the lateral van der Waals interaction between alkyl chains, and disordering of interfacial Au atoms, driven by the sulfur-gold interaction. We found that the sulfur atoms of the molecules bind at two distinct surface sites, and that the first gold surface layer contains gold atom vacancies (which are partially redistributed over different sites) as well as gold adatoms that are laterally bound to two sulfur atoms.

Defect states at the TiO2(110) surface probed by resonant photoelectron diffraction.

The charge distribution of the defect states at the reduced TiO(2)(110) surface is studied via a new method, the resonant photoelectron diffraction. The diffraction pattern from the defect state, excited at the Ti-2p-3d resonance, is analyzed in the forward scattering approach and on the basis of multiple scattering calculations. The defect charge is found to be shared by several surface and subsurface Ti sites with the dominant contribution on a specific subsurface site in agreement with density functional theory calculations.

Structure of a CH3S monolayer on Au(111) solved by the interplay between molecular dynamics calculations and diffraction measurements.

We have investigated the controversy surrounding the (sqrt[3] x sqrt[3]) R30 degrees structure of self-assembled monolayers of methylthiolate on Au(111) by first principles molecular dynamics simulations, energy and angle resolved photoelectron diffraction, and grazing incidence x-ray diffraction. Our simulations find a dynamic equilibrium between bridge site adsorption and a novel structure where 2 CH3S radicals are bound to an Au adatom that has been lifted from the gold substrate. As a result, the interface is characterized by a large atomic roughness with both adatoms and vacancies. This result is confirmed by extensive photoelectron and grazing incidence x-ray diffraction measurements.

Electronic properties of a pure and sodium-doped C(70) single layer adsorbed on Al polycrystalline surface.

Core level and valence band photoemission measurements combined with near edge x-ray absorption fine structure measurements were performed on a single C(70) layer adsorbed on polycrystalline Al (1 ML-C(70)/Al) (ML-monolayer), pure and doped with sodium atoms. The data obtained from the pure ML chemisorbed on Al surface show a semiconducting behavior of the system, which is characterized by a covalent bond between the adsorbate and the substrate. The same data show also that the C(70) molecules tend to orient themselves with the C(5v) axis perpendicular to the surface in analogy to what observed for 1 ML-C(70)/Cu(111). By doping the sample with sodium atoms a charge transfer from the alkali atoms to the lowest unoccupied molecular orbital (LUMO) of the C(70) molecules takes place, as underlined by the gradual increasing intensity of the C(70) LUMO peak as a function of doping. Nevertheless, no metallic phases are observed for any doping step.