Revisiting Bond Breaking and Making in EuCo2 P2 : Where are the Electrons?

X-ray absorption spectroscopy (XAS) was used to elucidate changes in the electronic structure caused by the pressure-induced structural collapse in EuCo2 P2 . The spectral changes observed at the L3 -edge of Eu and K-edges of Co and P suggest electron density redistribution, which contradicts the formal charges calculated from the commonly used Zintl-Klemm concept. Quantum-chemical calculations show that, despite the increase in the oxidation state of Eu and the formation of a weak P-P bond in the high-pressure phase, the electron transfer from the Eu 4f orbitals to the hybridized 5d and 6s states causes strengthening of the Eu-P and P-P bonds. These changes explain the increased electron density on P atoms, deduced from the P K-edge XAS spectra. This work shows that the formal electron counting schemes do not provide an adequate description of changes associated with phase transitions in metallic systems with substantial mixing of the electronic states.

A workflow for single-particle structure determination via iterative phasing of rotational invariants in fluctuation X-ray scattering.

Fluctuation X-ray scattering (FXS) offers a complementary approach for nano- and bioparticle imaging with an X-ray free-electron laser (XFEL), by extracting structural information from correlations in scattered XFEL pulses. Here a workflow is presented for single-particle structure determination using FXS. The workflow includes procedures for extracting the rotational invariants from FXS patterns, performing structure reconstructions via iterative phasing of the invariants, and aligning and averaging multiple reconstructions. The reconstruction pipeline is implemented in the open-source software xFrame and its functionality is demonstrated on several simulated structures.

Extreme Biomimetics: Designing of the First Nanostructured 3D Spongin-Atacamite Composite and its Application.

The design of new composite materials using extreme biomimetics is of crucial importance for bioinspired materials science. Further progress in research and application of these new materials is impossible without understanding the mechanisms of formation, as well as structural features at the molecular and nano-level. It presents a challenge to obtain a holistic understanding of the mechanisms underlying the interaction of organic and inorganic phases under conditions of harsh chemical reactions for biopolymers. Yet, an understanding of these mechanisms can lead to the development of unusual-but functional-hybrid materials. In this work, a key way of designing centimeter-scale macroporous 3D composites, using renewable marine biopolymer spongin and a model industrial solution that simulates the highly toxic copper-containing waste generated in the production of printed circuit boards worldwide, is proposed. A new spongin-atacamite composite material is developed and its structure is confirmed using neutron diffraction, X-ray diffraction, high-resolution transmission electron microscopy/selected-area electron diffraction, X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, and electron paramagnetic resonance spectroscopy. The formation mechanism for this material is also proposed. This study provides experimental evidence suggesting multifunctional applicability of the designed composite in the development of 3D constructed sensors, catalysts, and antibacterial filter systems.

2D/3D Metallic Nano-objects Self-Organized in an Organic Molecular Thin Film.

We present the fabrication and investigation of the properties of nanocomposite structures consisting of two-dimensional (2D) and three-dimensional (3D) metallic nano-objects self-organized on the surface and inside of organic molecular thin-film copper tetrafluorophthalocyanine (CuPcF4). Metallic atoms, deposited under ultrahigh vacuum (UHV) conditions onto the organic ultrathin film, diffuse along the surface and self-assemble into a system of 2D metallic overlayers. At the same time, the majority of the metal atoms diffuse into the organic matrix and self-organize into 3D nanoparticles (NPs) in a well-defined manner. The evolution of the morphology and electronic properties of such structures as a function of nominal metal content is studied under UHV conditions using transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HR-TEM), and photoelectron spectroscopy (PES) techniques. Using HR-TEM, we have observed the periodicity of atomic planes of individual silver NPs. The steady formation of agglomerates from individual single nanocrystallites with intercrystallite boundaries is observed as well. PES reveals generally weak chemical interactions between silver and the organic matrix and n-doping of CuPcF4 at the initial stages of silver deposition, which is associated with charge transfer from the 2D wetting layer on the basis of core-level spectra shift analysis.

X-ray absorption microscopy of bacterial surface protein layers: X-ray damage.

The electronic structure of individual sheets of the bacterial surface protein layer (S layer) of Bacillus sphaericus NCTC 9602 was studied using a photoemission electron microscope (PEEM) operating in near-edge X-ray absorption fine structure spectroscopy mode. The laterally resolved measurements performed at the C 1s, N 1s, and O 1s thresholds on fresh samples revealed characteristic differences compared to the laterally integrated data, where substrate contributions were taken along with the protein signals. During the PEEM experiments an irradiation-induced increase of the C-C bond density at the cost of the densities of the C-O and C-N bonds related to a rearrangement of the contributing atoms of the S layer deposited onto a Si substrate was observed. The critical irradiation doses for the C-O and C-N bond breaking and formation of the new C-C bonds were derived.

Photoemission and near-edge X-ray absorption fine structure studies of the bacterial surface protein layer of Bacillus sphaericus NCTC 9602.

The electronic structure of the regular, two-dimensional bacterial surface protein layer of Bacillus sphaericus NCTC 9602 has been examined by photoemission (PE) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Both the O 1s and the N 1s core-level PE spectra show a single structure, whereas the C 1s core-level spectrum appears manifold, suggesting similar chemical states for each oxygen atom and also for each nitrogen atom, while carbon atoms exhibit a range of chemical environments in the different functional groups of the amino acids. This result is supported by the element-specific NEXAFS spectra of the unoccupied valence electronic states, which exhibit a series of characteristic NEXAFS peaks that can be assigned to particular molecular orbitals of the amino acids by applying a phenomenological building-block model. The relative contributions of the C-O, C-N, and C-C bond originating signals into the C 1s PE spectrum are in good agreement with the number ratios of the corresponding bonds calculated from the known primary structure of the bacterial surface protein. First interpretation of the PE spectrum of the occupied valence states is achieved on the basis of electronic density-of-states calculations performed for small peptides. It was found that mainly the pi clouds of the aromatic rings contribute to both the lowest unoccupied and the highest occupied molecular orbitals.

Insight into bio-metal interface formation in vacuo: interplay of S-layer protein with copper and iron.

The mechanisms of interaction between inorganic matter and biomolecules, as well as properties of resulting hybrids, are receiving growing interest due to the rapidly developing field of bionanotechnology. The majority of potential applications for metal-biohybrid structures require stability of these systems under vacuum conditions, where their chemistry is elusive, and may differ dramatically from the interaction between biomolecules and metal ions in vivo. Here we report for the first time a photoemission and X-ray absorption study of the formation of a hybrid metal-protein system, tracing step-by-step the chemical interactions between the protein and metals (Cu and Fe) in vacuo. Our experiments reveal stabilization of the enol form of peptide bonds as the result of protein-metal interactions for both metals. The resulting complex with copper appears to be rather stable. In contrast, the system with iron decomposes to form inorganic species like oxide, carbide, nitride, and cyanide.

Solvothermal synthesis of hydrophobic chitin-polyhedral oligomeric silsesquioxane (POSS) nanocomposites.

Chitinous scaffolds isolated from the skeleton of marine sponge Aplysina cauliformis were used as a template for the deposition of polyhedral oligomeric silsesquioxanes (POSS). These chitin-POSS based composites with hydrophobic properties were prepared for the first time using solvothermal synthesis (pH 3, temp 80 °C), and were thoroughly characterized. The resulting material was studied using scanning electron microscopy, Raman spectroscopy, X-ray photoelectron spectroscopy and thermogravimetry. A mechanism for the chitin-POSS interaction after exposure to these solvothermal conditions is proposed and discussed.

An extreme biomimetic approach: hydrothermal synthesis of ß-chitin/ZnO nanostructured composites.

ß-Chitinous scaffolds isolated from the skeleton of marine cephalopod Sepia officinalis were used as a template for the in vitro formation of ZnO under conditions (70 °C) which are extreme for biological materials. Novel ß-chitin/ZnO film-like composites were prepared for the first time by hydrothermal synthesis, and were thoroughly characterized using numerous analytical methods including Raman spectroscopy, HR-TEM and XRD. We demonstrate the growth of hexagonal ZnO nanocrystals on the ß-chitin substrate. Our chitin/ZnO composites presented in this work show antibacterial properties against Gram positive bacteria and can be employed for development of inorganic-organic wound dressing materials.

Isolation and identification of chitin in the black coral Parantipathes larix (Anthozoa: Cnidaria).

Until now, there is a lack of knowledge about the presence of chitin in numerous representatives of corals (Cnidaria). However, investigations concerning the chitin-based skeletal organization in different coral taxa are significant from biochemical, structural, developmental, ecological and evolutionary points of view. In this paper, we present a thorough screening for the presence of chitin within the skeletal formations of a poorly investigated Mediterranean black coral, Parantipathes larix (Esper, 1792), as a typical representative of the Schizopathidae family. Using a wide array variety of techniques ((13)C solid state NMR, Fourier transform infrared (FTIR), Raman, NEXAFS, Morgan-Elson assay and Calcofluor White Staining), we unambiguously show for the first time that chitin is an important component within the skeletal stalks as well as pinnules of this coral.

Real-time study of the modification of the peptide bond by atomic calcium.

Strong chemical interaction between bacterial surface protein layers and calcium atoms deposited in situ on top was revealed by means of photoemission spectroscopy. The interaction appears to mainly happen at the oxygen site of the peptide bonds and involves a large charge transfer from Ca 4s states into the peptide backbone. Chemical kinetics of this reaction was characterized using time-dependent valence band photoemission, and the reaction rate constant was determined.

Electronic structure of genomic DNA: a photoemission and X-ray absorption study.

The electronic structure of genomic DNA has been comprehensively characterized by synchrotron-based X-ray absorption and X-ray photoelectron spectroscopy. Both unoccupied and occupied states close to the Fermi level have been unveiled and attributed to particular sites within the DNA structure. A semiconductor-like electronic structure with a band gap of approximately 2.6 eV has been found at which the pi and pi* orbitals of the nucleobase stack make major contributions to the highest occupied and lowest unoccupied molecular orbitals, respectively, in agreement with previous theoretical predictions.

X-ray damage in protein-metal hybrid structures: a photoemission electron microscopy study.

Bacterial surface layer protein sheets (S layer) coated with an ultrathin cobalt or silver film were studied by means of laterally resolved near-edge X-ray absorption fine structure spectroscopy performed by photoemission electron microscopy. Comparison with results obtained on pristine S layers allowed us to characterize both chemical interaction and X-ray damage in these protein-metal hybrid systems. In particular, we found that besides direct damage upon exposure to X-ray radiation the biomolecules experience additional contribution of the deposited metals, by low-energy electron generation in the metal particles.

Mineralization of the metre-long biosilica structures of glass sponges is templated on hydroxylated collagen.

The minerals involved in the formation of metazoan skeletons principally comprise glassy silica, calcium phosphate or carbonate. Because of their ancient heritage, glass sponges (Hexactinellida) may shed light on fundamental questions such as molecular evolution, the unique chemistry and formation of the first skeletal silica-based structures, and the origin of multicellular animals. We have studied anchoring spicules from the metre-long stalk of the glass rope sponge (Hyalonema sieboldi; Porifera, Class Hexactinellida), which are remarkable for their size, durability, flexibility and optical properties. Using slow-alkali etching of biosilica, we isolated the organic fraction, which was revealed to be dominated by a hydroxylated fibrillar collagen that contains an unusual [Gly-3Hyp-4Hyp] motif. We speculate that this motif is predisposed for silica precipitation, and provides a novel template for biosilicification in nature.

Electronic structure of regular bacterial surface layers.

We report photoemission and near-edge x-ray absorption fine structure measurements of the occupied and unoccupied valence electronic states of the regular surface layer of Bacillus sphaericus, which is widely used as the protein template for the fabrication of metallic nanostructures. The two-dimensional protein crystal shows a semiconductorlike behavior with a gap value of approximately 3.0 eV and the Fermi energy close to the bottom of the lowest unoccupied molecular orbital. We anticipate that these results will open up new possibilities for the electric addressability of biotemplated low-dimensional hybrid structures.