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.

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.

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.

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.

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.

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.

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.

Atomically resolved images from near node photoelectron holography experiments on Al(111).

Szöke's concept for electron holography is hampered by forward scattering that dominates electron diffraction from electron point sources below the surface top layer. Forward scattering was proposed to be suppressed if the anisotropic nature of the electron source wave is exploited [T. Greber and J. Osterwalder, Chem. Phys. Lett. 256, 653 (1996)]. Experiments show a strong suppression of forward scattering in Al(111) if Al 2s photoelectrons (E(kin) = 952 eV) are measured near the nodal plane of the outgoing p wave. The holographic reconstruction from such diffraction data provides three dimensional images of atomic sites in unit cells with a size of more than 10 A.

Analysis of a bioactive synthetic analogue of tuftsin by tandem mass spectrometry: anomalous fast atom bombardment activated processes.

Fast atom bombardment (FAB) tandem mass spectrometry has been used to analyse the biologically potent, partially modified retro-inverso (PMRI) synthetic isomer of tuftsin: this compound represents the active peptide of the fraction of gamma-globulin (leukokinin) which binds specifically to blood neutrophilic leukocytes and monocytes. Protonated molecules and fragment ions were collisionally dissociated at low energies in a triple-quadrupole mass spectrometer to yield a complete picture of the reactions that occur in the condensed and in the gas phase. The study shows that, when retro-inversion is within the N-terminal amino acid, charge localization at the basic sites (possibly at the N-terminus) induces a marked decomposition of the molecule, the loss of ammonia being the most favourable fragmentation process. Also, artifacts are formed in the liquid phase via bimolecular reactions promoted by the high-energy beam. The findings indicate that despite the fact that PMRI isomers of this type are stable against exo-peptidases and also stable under acidic conditions, they appear to be labile under conditions where the energy deposition, due to FAB is necessarily high.

Solution conformation of tuftsin.

Tuftsin, a natural linear tetrapeptide (Thr-Lys-Pro-Arg) of potential antitumor activity, has been studied in DMSO-d6 solution by 2D NMR spectroscopy. 1H and 13C spectra show the presence of two families of conformations characterized by a trans or cis Lys-Pro bond, respectively. The family of conformers containing the cis peptide bond is a mixture of extended structures as expected for a short linear peptide. On the contrary, the trans isomer appears to be a rigid, folded conformer, as indicated by crucial NOEs and by the exceptionally low temperature coefficient of Arg NH. Analysis of the solution data by means of energy calculations leads to a unique structure, characterized by a Lys-Pro inverse gamma-turn.

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.

Mycobacterial heat-shock proteins as carrier molecules.

We have previously shown that the priming of mice with live Mycobacterium tuberculosis var. bovis (Bacillus Calmette-Guérin, BCG) and immunization with the repetitive malaria synthetic peptide (NANP)40 conjugated to purified protein derivative (PPD), led to the induction of high and long-lasting titers of anti-peptide IgG antibodies, overcoming the requirement of adjuvants and the genetic restriction of the antibody response to the peptide (Lussow et al., Proc. Natl. Acad. Sci. USA 1990. 87:2960). This initial work led us to the following observations. BCG had to be live for priming to lead to the induction of anti-peptide antibodies. Surprisingly, priming with other living microorganisms which chronically infect the macrophage (e.g. Salmonella typhimurium and Leishmania major) also induced anti-peptide antibodies in mice immunized with PPD-(NANP)40 conjugate. It was, thus, hypothesized that molecules expressed during active infection and also known to be highly conserved between species, namely the heat-shock proteins (hsp), could mediate the T cell sensitization required for the production of anti-peptide antibodies. In fact, when the PPD protion of the conjugate was replaced by a highly purified recombinant protein corresponding to the 65-kDa (GroEL-type) hsp of M. bovis, this resulted in the production of anti-(NANP) IgG antibodies in BCG-primed mice, irrespective of the major histocompatibility complex-controlled responsiveness to the (NANP) sequence itself. Further, similar induction of anti-peptide antibody response was also obtained with a recombinant 70-kDa (DnaK-type) hsp of M. tuberculosis, but not with a small molecular mass (18 kDa) of M. leprae. Finally, an adjuvant-free carrier effect for anti-peptide IgG antibody production in BCG-primed mice, was also exerted by the GroEL hsp of Escherichia coli. This finding that hsp can act as carrier molecules without requiring conventional adjuvants is of potential importance in the development of vaccine strategies.

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.

Large-scale purification of the synthetic peptide fragment 163-171 of human interleukin-beta by multi-dimensional displacement chromatography.

Multi-dimensional chromatography has been used successfully in the displacement mode for the purification of the synthetic peptide H-Val-Gln-Gly-Glu-Glu-Ser-Asn-Asp-Lys-OH, the fragment 163-171 of human interleukin-beta. This peptide can mimic several of the in vivo and in vitro immunostimulatory activities of the entire protein, except for the inflammatory effect. A large-scale procedure has been developed to purify the synthetic peptide by reversed-phase (RP) and ion-exchange (IE) displacement chromatography (DC) in a single run without any pretreatment. Masses from 100 mg to about 35 g of the unpurified compounds synthesized by a solid-phase technique on a Merrifield-type resin and obtained by acidolytic cleavage from the solid support, can be purified in this way. In the RP-DC mode the carrier and the displacer were aqueous solutions of 0.1% trifluoroacetic acid and 50 mM benzyltributylammonium chloride, respectively, whereas in the IE-DC mode the carrier was water and the displacer 50 mM ammonium citrate solution. RP-DC and IE-DC were also performed in series by directing the effluent of the RP column onto the IE column. Peptide purities and recoveries greater than 96 and 90%, respectively, were obtained.

Toward the elucidation of the mechanism of attachment and entry of malaria sporozoites into cells: synthetic polypeptides from the circumsporozoite protein of Plasmodium falciparum bind Ca2+ and interact with model phospholipid membranes.

Through the joint use of CD, Fourier transform ir (FTIR), and attenuated total reflectance FTIR we have found that synthetic polypeptide models of the Plasmodium falciparum circumsporozoite (CS) protein repeat domain bind calcium ions in helicogenic environments. Ca(2+)-(NANP)n complexes (n greater than or equal to 20) interact vectorially with model phospholipid membranes orienting their polypeptide axes preferentially along those of the lipid acyl chains. It is proposed that the P. falciparum CS protein central region, rather than acting as a molecular lure helping the parasite to evade host immune control, plays, as a specific Ca2+ macroligand, a critical functional role during attachment, invasion, and development of the malaria parasite in the hepatic cell.

Synthetic peptides for Plasmodium vivax malaria sero-epidemiology. Application of Fmoc-polyamide and displacement chromatography.

The immunodominant epitope of Plasmodium vivax, one of the major causative agents of malaria in man, consists of the tandem repetitions of a nonapeptide sequence, AspArgAlaAsp/AlaGlyGlnProAlaGly, with Asp (variant d) or Ala (variant a), in the fourth position. Synthetic peptides corresponding to the P. vivax epitope, containing a different number of nonapeptide sequences, were prepared by solid-phase synthesis according to the Fmoc-polyamide method. Three peptides, containing 1, 2, and 4 copies of the d variant, were assembled on the gel polymer; none of these peptides, however, was suitable for P. vivax sero-epidemiology. A 45-peptide containing both the d and a variants, ddaad, was prepared by continuous-flow Fmoc-polyamide (flow-polyamide). Among the cleavage procedures evaluated for the removal of the five Mtr groups only TFMSA/TFA/1,2-ethanedithiol (1:89:10 by vol) brought deblocking to completion; a substantial level of impurities originated, however, from these procedures. The product was purified by reversed-phase displacement chromatography, a technique only recently applied to peptides, which shows distinct advantages over conventional, linear elution chromatography. In a single experiment, 107 mg of the crude mixture were loaded onto an analytical column (250 x 4 mm), obtaining in purified form 85% of the desired material present in the sample. An ELISA test base on the ddaad peptide was developed and is being applied to the sero-epidemiology of P. vivax malaria.