Researchers deciphering the mechanism of sliding of DNA clamps, central players in DNA replication and repair

The genetic information is encoded in long chains of deoxyribonucleic acid (DNA) molecules packaged into chromosomes in the cell nucleus. Every time a cell replicates itself, the DNA needs to be duplicated. Critical players in this process are the so-called DNA clamps, ring-shaped proteins that slide onto the DNA double helix and anchor the polymerases, the enzymes that replicate DNA, onto the genomic template. While two-decade studies revealed the importance of DNA sliding clamps in many cellular processes, key mechanisms of their function at the molecular level remained elusive.
Proliferating Cell Nuclear Antigen (PCNA), or the eukaryotic DNA clamp, is a ring-shaped protein that encircles DNA and anchor the polymerases, the enzymes that duplicate DNA. For the first time, researchers have deciphered how PCNA moves on DNA, a spiral movement that poses the protein in the correct orientation to bind the polymerase.)

A joint collaboration involving three research teams and headed by the Structural Biology Laboratory at Elettra-Sincrotrone Trieste (Matteo De March, Silvia Onesti and Alfredo De Biasio) revealed how the human DNA clamp PCNA (Proliferating Cell Nuclear Antigen) moves on DNA. Employing a combination of structural and computational approaches, and also making use of the X-ray beamline XRD1 at Elettra as a CERIC facility, De Biasio and colleagues discovered that PCNA slides on DNA through a spiral motion that keeps the orientation of PCNA competent for binding to the polymerase.
Due to the critical role of DNA sliding clamps in cell proliferation, understanding their mechanics at the molecular level may contribute to defining novel drug targets for anti-cancer therapy. Therefore, the insight provided by this study is also important for potential future medical applications.

  • Original article: M. De March, N. Merino, S. Barrera-Vilarmau, R. Crehuet, S. Onesti, F. J. Blanco, A. De Biasio, Structural basis of human PCNA sliding on DNA, in Nature Communications, 2017, 8:13935, doi:10.1038/ncomms13935

New structures of DNA discovered, for a better understanding of the mechanisms of immune response activation

Prof. Janez Plavec, Director of the Slovenian CERIC facility at the National Institute of Chemistry in Ljubljana, significantly contributed to an important achievement that was published in the prestigious scientific journal Nature Communications. The field is that of DNA research and represents a breakthrough, since it discovers hitherto unknown structures of DNA and thus improves the understanding of DNA and the mechanism of immune response activation.

Structural studies with the use of solution-state nuclear magnetic resonance (NMR) spectroscopy have shown that oligonucleotides containing AGCGA repeats fold into structures that belong to a new structural family which we named AGCGA-quadruplexes. The structural core of the family is comprised out of four AGCGA repeats that form quartet planes. AGCGA-quadruplexes contain unusual structural elements such as GCGC and AGCGA quartets and are additionally stabilized with noncanonical base pairs. To the best of our knowledge, we have described GAGA-quartets formed by two G-A pairs in N1-N7 carbonyl amino geometry for the first time. G-G base pairs in N1-carbonyl symmetric geometry formally form loop regions and connect quartets inside AGCGA-quadruplexes. It is especially interesting that even though guanine residues are very common in oligonucleotides that form AGCGA-quadruplexes they in turn do not contain G-quartets and are insensitive to the presence of different cations such as Na+, K+ and NH4+. This property makes the AGCGA-quadruplex structural family unique compared to the related and more widely known family of G-quadruplexes. With bioinformatics studies we have shown that AGCGA rich sequences are found in regulatory regions of 39 human genes responsible for basic cellular processes that are related to neurological disorders, cancer and abnormalities in bone and cartilage development. With the use of NMR and CD spectroscopy we have confirmed that 46 oligonucleotides found in regulatory regions of the above mentioned 39 human genes fold into AGCGA-quadruplexes. The results of the study are published in the journal Nature Communications.

  • Original article: V. Kocman & J. Plavec, Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions. Nat. Commun. 2017, 8, 15355. doi:10.1038/ncomms15355

Research gives new hints for anti-inflammatory drug delivery

This work, conducted by the research group around Prof. Andrea Mele, aimed at testing exploring the capability of two types of nanosponges for the entrapment and delivery of Ibuprofen, the Active Principle Ingredient (API) of many anti-inflammatory drugs.

Nanosponges are formed from molecules that link to each other forming macromolecular structures, characterised by the presence of cavities that can accommodate other molecules, like Ibuprofen in this case. In this way, when the nanosponge is loaded with the drug, it becomes a carrier. The carrier provides a better stability to the drug and allows to control the delivery process. In some cases, the nanosponge can even help to select the most active one from a group of molecules.
The dynamics and interactions of two formulations of cyclodextrin nanosponges with Ibuprofen, were studied with a particular Nuclear Magnetic Resonance (NMR) technique (cross-polarisation magic angle spinning) and X-Ray Diffraction, available at CERIC-ERIC.
The authors concluded that the repertoire of NMR methods used was helpful to monitor the effective state of the drug in the carrier and of the polymer carrier in the presence of the guest drug. In a counterintuitive way, Ibuprofen was found to form small aggregates (dimers), in turn organized in small crystalline domains confined in the CDNS cavities. CDNS retains its structure which does not undergo changes upon addition of the drug.

Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy

Anomalous diffusion of Ibuprofen in cyclodextrin nanosponge hydrogels

However, the NMR measurement pointed out that the dynamic regime of the polymer indeed changed. This finding can be used as a fingerprint of the formation of aggregation, at molecular level, between the drug and the host polymer rather than a pure physical conglomerate.

  • Original article: M. Ferro, F. Castiglione, N. Pastori, C. Punta, L. Melone, W. Panzeri, B. Rossi, F. Trotta, A. Mele, Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy, in Beilstein J. Org. Chem. 2017, 13, 182–194

Multi-method approach sheds light on the potential of plants to attenuate metals’ load in natural water resources

Extensive industrial mining often causes environmental problems. Many former mining sites around the world are heavily polluted with poisonous heavy metals that make the areas dangerous to live in, often for decades. For this reason, the last 25 years saw a rise in the development of remediation technologies to make those polluted zones habitable again. But the processes that the heavy metals undergo over a long time in a natural environment are complex and not completely understood, yet. Especially the influence of the exchange between the geosphere, the soil and water, and the biosphere, the plants and organisms, is mainly unknown. On the other hand, an understanding of these biosphere-geosphere interactions could lead to a significant step forward in the development of sustainable remediation techniques.
The research team around Giovanni De Giudici from the University of Cagliari, in Sardinia – Italy, is taking up the challenge of understanding how plants influence the behaviour of heavy metals in polluted rivers.

EDS analysis (top) and SEM image (bottom) of framboidal iron sulphide on root of Phragmites australis. b) Ordinary light stereo-microscope image (top) and LEXRF maps of Fe, Si, Zn and Al of Phragmites australis (bottom)

Together with researchers from the U.S. Geological Survey, they performed a large multi-technique study on heavy metals in the Sardinian river of Rio San Giorgio [1]. The area of that river has been exposed to heavy Lead and Zinc mining since centuries, up to 20 years ago. For this reason, the area has been heavily polluted. De Giudici’s study focuses on the so-called hyporheic zone, which is the shallow shore of the river. Here the water flows naturally very slow and the vegetation is very dense. This allows a maximum interaction between the water and the surrounding environment. The researchers were taking plant and soil samples from this zone at different point of the river to see how the pollutants are distributed.
For the detection of pollutants in the samples, they used X-ray microscopy at the TWINMIC beamline and X-ray absorption spectroscopy at the XAFS beamline, both from the CERIC Italian Partner Facility at Elettra in Trieste. The combination of the two techniques enables the simultaneous determination of the concentration and the chemical state of heavy metals in different parts of the soil and the plant. This allows conclusions about how much pollutant is filtered from the water and in which composition it is stored in the plants and soil.
As a result of this study, the researchers could create a map of pollutants in the hyphoreic zone of the river. A big part of the heavy metals found in the water is oxidized and stored in the plants’ roots, but some of it is also found in the stem and the leaves. An additional result was particularly surprising. The scientists found a high concentration of the mineral pyrite in the soil around the plants’ roots. This iron-containing mineral suggests that the plant is influencing the chemical environment and supports chemical processes that lead to the storage of poisonous heavy metals into non poisonous minerals. It has been estimated that this effect can lead to an apparent decrease in Zn load up to 60%. This effect was by now unknown and, when fully investigated, might open new ways of using plants as more effective filters and cleaners in polluted areas.

  • Original article: G. De Giudici, C. Pusceddu, D. Medas, C. Meneghini, A. Gianoncelli, V. Rimondi, F. Podda, R. Cidu, P. Lattanzi, R. B. Wanty, B. A. Kimball, The role of natural biogeochemical barriers in limiting metal loading to a stream affected by mine drainage, Appl. Geochem. 76, 2017, 124-135

Deeper insight into platinum-graphene catalysts: towards filtering of exhaust gases and synthesis of energy vectors

The chemical transformation of carbon monoxide (CO) is one of the most important processes, not only in factories but also in everyday life. Its applications range from the oxidation of poisonous CO to non-poisonous carbon dioxide (CO2) in engine exhaustions, to the so-called “water-gas shift reaction”, where hydrogen, e.g. for fuel cells, is produced by a reaction between carbon monoxide and water. To make these reactions energetically efficient, catalysts based on platinum are widely used. Since platinum is a very expensive and rare precious metal, a strong focus in industrial and academic research is given to the development of catalysts with low platinum content. An approach to optimize platinum catalysts is to exploit the special properties of nano-sized particles on suitable supporting materials like graphene. In this perspective, it is of high importance to understand the interactions between carbon monoxide, the supporting material, and platinum.

The collaboration among three research teams of the University of Trieste, led by Prof. Giovanni Comelli, Prof. Maria Peressi, and Dr. Erik Vesselli, respectively, yielded a breakthrough in understanding a part of these interactions.

Structure and adsorption properties of Pt nanoparticles as obtained from microscopy, spectroscopy, and theoretical approaches

By combining state-of-the art experimental and theoretical approaches with access, within the framework of a CERIC experiment, to instruments available at the Czech Partner Facility, they studied the change of such platinum catalysts on a graphene support when they are exposed to carbon monoxide. They exploited a new near ambient pressure photoelectron spectrometer (NAP-XPS) that allows measurements under almost realistic reaction conditions. Their measurements shed light into details about the mechanisms through which carbon monoxide weakens the connection between platinum and the graphene support. This leads to a coalescence, basically a clotting, of the small particles to larger clusters that might affect the catalytic performance. This effect appears to be size-dependent, and relates with the onset of properties stemming from quantum mechanics due to the small size of the particles. The structure of the particles is also affected, and a peculiar diffusion mechanism takes place, yielding migration of carbon monoxide through the graphene sheet.

These important results mark a step forward in understanding the complex reactions that happens during the catalytic process. This understanding will help to design more efficient catalysts for a wide variety of technical applications.

  • Original article: N. Podda, M. Corva, F. Mohamed, Z. Feng, C. Dri, F. Dvorák, V. Matolin, G. Comelli, M. Peressi, E. Vesselli, Experimental and theoretical investigation of the restructuring process induces by CO at Near Ambient Pressure: Pt Nanoclusters on Graphene/Ir (111); ACS Nano 11 (2017) 1041)

Structure of a Stable G-Hairpin*

An 11-nt long G-rich DNA oligonucleotide, 5′-d(GTGTGGGTGTG)-3′, corresponding to the most abundant sequence motif in irregular telomeric DNA from Saccharomyces cerevisiae (yeast) has been shown to fold into a G-hairpin. The first atomic resolution structure of a stable G-hairpin formed by a natively occurring DNA sequence demonstrates a novel type of mixed parallel/antiparallel fold-back DNA structure, which is stabilized by dynamic G:G base pairs that transit between N1-carbonyl symmetric and N1-carbonyl, N7-amino base-pair arrangements.
G-hairpin is a thermodynamically stable structure with a rather complex topology that includes a chain reversal arrangement of the backbone in the center of the continuous G-tract and 3′-to-5′ stacking of the terminal residues. The structure reveals previously unknown principles of the folding of G-rich oligonucleotides that could be applied to the prediction of natural and/or the design of artificial recognition DNA elements. The structure also demonstrates that the folding landscapes of short DNA single strands is much more complex than previously assumed.

The described paper has been highlighted in JACS Spotlights

  • Original article: M. Gajarský, M. Lenarčič Živković, P. Stadlbauer, B. Pagano, R. Fiala, J. Amato, L. Tomáška, J. Šponer, J. Plavec, L. Trantírek, Structure of a Stable G‑Hairpin, J. Am. Chem. Soc. 2017, 139 (10), 3591-3594. doi: 10.1021/jacs.6b10786, COBISS ID 6101274)

Study of ancient glazed pottery from Azerbaijan confirms the need for a multi-technique approach in cultural heritage research*

The combination of several techniques is fundamental to analysing different aspects of archaeological findings. An interesting example showing the importance of applying a multi-technique approach in this field is that of the latest research conducted by the research group to which the CERIC user Valentina Venuti belongs, which focused on eight archaeological pottery fragments from the medieval ruins of the Agsu archaeological site in Azerbaijan.

The group applied a combination of complementary techniques: optical microscopy (OM), scanning electron microscopy – energy dispersive spectroscopy (SEM-EDS) and prompt gamma activation analysis (PGAA at the Hungarian CERIC partner facility – Budapest Neutron Centre) to define the raw materials and pigments used for the production and decoration of the samples, and X-ray diffraction (XRD) to assess their firing temperature.

SEM micromorphological details of glaze and ceramic body

The data obtained suggest the presence of different production technologies and raw materials (quartz, plagioclase, feldspar and hematite in one group of samples, quartz and plagioclase in the second one), probably due to the site position at the crossroad of commercial routes. Moreover, XRD analysis suggested that the original calcareous clay of both groups of samples was fired at temperatures higher than 850°C. Only for one group of samples was it possible to hypothesize Chinese production and provenance. However, more samples (both pottery fragments and local clays) need to be studied in order to confirm this hypothesis.

The work, which can overall be considered a milestone for future archaeometric studies in this area, is a first step towards further sampling campaigns about both archaeological and geological specimens needed for reconstructing the provenance of artefacts.

  • Original article V. Crupi, Z. Kasztovszky, F. Khalillil, M. F. La Russa, A. Macchia, D. Majolino, B. Rossi, N. Rovella, S. A. Ruffolo and V. Venuti, Evaluation of complementary methodologies applied to a preliminary archaeometric study of glazed pottery from Agsu (Azerbaijan), International Journal of Conservation Science, Vol. 7, Special issue 2, 2016:901-912

Scientists test caffeine as a model system for developing and designing new hydrogels for biomedicine, cosmetics and environmental control*

Hydrogels are a special class of materials that have a particular three-dimensional structure, with internal spaces that can host guest molecules or water solutions containing active molecules. This structure allows hydrogels to absorb large amounts of water without losing their elasticity. Hydrogels, made of biopolymers like sugar chains, can be used as superabsorbers for cosmetics and medical purposes, such as wound-dressing, and even as scaffold for tissue engineering. They have recently attracted some interest as model systems for “smart” hydrogels that are able to react with their environment (e.g. human skin) in a programmed and intelligent manner or for drug delivery.

The effect of guest-matrix interactions on the solvation of cyclodextrin-based polymeric hydrogels is studied by UV Raman experiments

In this context, the working group around Barbara Rossi from the Italian CERIC facility, Elettra Sincrotrone Trieste, together with her co-workers from the University of Messina and Politecnico of Milan, have developed a hydrogel based on natural cyclodextrin – a particular derivative of glucose – that act as a nano-sponge. They recently published a study that investigates the mechanisms of entrapment, diffusion and release of guest molecules such as pharmaceutical active ingredients on these nano-sponges. As a model drug, they used the simple and well-known caffeine molecule. They used UV resonant Raman-Spectroscopy to analyse the structure of the model under different conditions. This method uses highly intensive ultra-violet light to monitor vibrations of the carbon atoms backbone within the nano-sponges. These vibrations are influenced by various factors, e.g. water uptake, drug loading and temperature.

For Raman spectroscopy, Rossi and her team used the CERIC IUVS instrument based at Elettra. They loaded the nano-sponges with various concentrations of caffeine at different temperatures. During their measurements, they discovered that caffeine significantly changes the temperature dependent properties of the nano-sponges. This shows for the first time that caffeine is not simply loaded into the structure of this special kind of hydrogel but actively changes the structure and the properties of the hydrogel. Furthermore, the molecular insights provided by UV-Raman spectroscopy for the first time allowed description and quantification of the caffeine induced structural changes within this type of nano-sponge. This valuable knowledge will enable further development of the dextrin-based hydrogels and will help in the design of new strategies to control the loading, diffusion and release rates of bioactive molecules inside hydrogels for future drug delivery applications.

  • Original article: B. Rossi, V. Venuti, F. D'Amico, A. Gessini, A. Mele, C. Punta, L. Melone, V. Crupi, D. Majolino and C. Masciovecchio, Guest-matrix interactions affect the solvation of cyclodextrinbased polymeric hydrogels: an UV Raman scattering study in Soft Matter, 2016, DOI: 10.1039/C6SM01647B

Scientists applied a new method for drugs quality control, purer medicines and a better health*

Stressful lifestyle results in many cardio-vascular diseases that are nowadays among main causes of death. A way to overcome this problem is to study, design and produce the purest medications as possible in order to reduce their side effects.
Nevertheless, manufacturing of pure drugs is very expensive and methodologies are limited to prove effective purity indicating impurities of pharmaceuticals below the detecting limit. The team of scientists led by Aden Hodzic, scientific and technology transfer officer at CERIC-ERIC, has applied a novel way to better test and control the purity of medicines and their structure by simultaneously analyzing the thermal behavior, purity, and structural properties of active pharmaceutical ingredients (APIs).

SAXS heating scans spectra of pentoxifylline in the temperature range of 80 to 140°C: a SAXS heating scan, b) SAXS scattered intensity versus temperature. (SAXS exposure time one minute per frame, which corresponds to two°C per frame).

The international team of researchers combined both Small- and Wide-Angle X-ray Scattering (SWAXS) techniques with the Differential Scanning Calorimetry (DSC), with the goal to conduct API purity quality control of pentoxifylline, a synthetic drug used for the treatment of peripheral vascular diseases, the management of cerebrovascular insufficiency, sickle cell disease and diabetic neuropathy. SWAXS gives information about the structure of the analyzed material, i.e. API polymorphism, whereas DSC deals with thermodynamic and calorimetric properties indicating thermal drug transition, which gives again information about drug purity. The idea to combine these techniques in one single analytical tool for a simultaneous analysis of these aspects of the material has demonstrated to be very effective for ensuring a complete and reliable quality control of medicals before their commercialization. Indeed, a strict testing to ensure the absence of destructive impurities is highly relevant for any further pharmaceutical procedure. The effectiveness of the experimental method, highlighting both the thermodynamic and the structural changes of APIs related to purity when metabolized, will guarantee better medicines for us and for our health.

The research has been the result of a scientific collaboration between CERIC-ERIC, the Graz University of Technology, the Research Centre for Pharmaceutical Engineering, the Institute of Pharmaceutical Sciences at the University of Graz and the company GL-Pharma. SWAXS and DCS are available also in CERIC laboratories at the Austrian beamline installed at Elettra in Trieste, Italy.

  • Original article: A. Hodzic, M. Kriechbaum, S. Schrank, F. Reiter, Monitoring of Pentoxifylline Thermal Behavior by Novel Simultaneous Laboratory Small and Wide X-Ray Scattering (SWAXS) and Differential Scanning Calorimetry (DSC), published on PLOS One, Volume 11, Issue 7, July 2016, Article number e0159840

How to preserve our cultural heritage? Scientists assess the firing conditions of old fired-clay bricks to find the most suitable restoration materials*

A research team around Alberto Viani from the Institute of Theoretical and Applied Mechanics in the Czech Republic performed a study to find the correlation between the structure of old fired-clay bricks and their firing temperature during the manufacturing process, in order to help in the replacement of damaged bricks for restoring some objects of our priceless cultural heritage.

Fired-clay bricks have been one of the most widespread construction materials in Europe. Their use flourished in the 19th century, when they were employed in the construction of a huge number of buildings. Most of them still survive but have endured a number of different environmental conditions over the years. The preservation of these often culturally important buildings is therefore a challenge. A widely accepted approach in cultural heritage restoration is to use the best compatible materials. To this end, the structural characterization of the original bricks is important in order to choose the best replacement material and prevent further damage to buildings. The results of this study were recently published in the Journal of Materials Characterization and in Brick and Block Masonry – Trends, Innovations and Challenges.

The research team investigated a number of bricks from two historical production sites in the Czech Republic, made at different firing temperatures for different purposes (masonry and chimney bricks). In addition to common mineralogical analysis methods such as electron microscopy, X-ray diffraction and porosimetry, they used the small angle neutron scattering (SANS) technique.

Optical microscope image in cross-polarised light of sample T (a) and U5 (b) in thin section

Since neutrons can penetrate deeply into matter, they are an ideal tool for the investigation of a dense porous system, such as fired bricks, ceramics and metals. SANS performed at the CERIC Hungarian facility, the Budapest Neutron Centre, therefore enabled characterization of the micro and nanostructure of bricks and information to be obtained about both their surface and their inner structure.

As a result of the study, the scientists could show that the amount of hematite – a mineral that is formed during the burning process – may be an indicator of the firing temperature used during the production process. Moreover, at the 16th International Brick and Block Masonry Conference in Padova (Italy), they showed the existence of an empirical relationship between the surface area per unit volume of pores obtained by SANS and the firing temperature. SANS was used in combination with a number of other standard techniques for the study of historical fired-clay bricks, confirming that it is a very effective tool for their characterization. Thanks to its efficiency, it greatly reduces the number of methods necessary to analyze old bricks and it may help in finding and/or producing suitable replacement materials for the preservation of valuable objects of the cultural heritage.

  • Original article - 1: A. Viani, K. Sotiriadis, A. Len, P. Šašek, R. Ševčík, Assessment of firing conditions in old fired-clay bricks: The contribution of X-ray powder diffraction with the Rietveld method and small angle neutron scattering, published in Materials Characterization, 116 (2016) 22-43
  • Original article - 2: A. Viani, K. Sotiriadis, P. Šašek, R. Ševčík, A. Len. Characterization of historical fired clay bricks with small angle neutron scattering. In: Modena C., da Porto F., Valluzzi M.R. (eds.), Proceedings of the 16th International Brick and Block Masonry Conference, Padova, Italy, June 26th-30th, 2016, Taylor & Francis Publications, Milton Park, 2016.

A clearer understanding of the role of zinc in glass structure brings the optimization of electronic displays a step forward*

Glasses are traditionally based on silicon (Si) but can also be formed by other elements, such as boron (B) and molybdenum (Mo). This is the case of boromolybdate glasses, which can be doped with other elements to change their properties. These glasses also contain zinc (Zn) and, in comparison to traditional silicon based glasses, they have high electrical conductivity and a lower melting point. This makes them interesting for applications in consumer electronics such as TVs and smartphone touch displays. Although boromolybdate glasses are already widely used, some questions on their atomic structure are still open. In particular, the exact role of zinc within the glass was not yet completely clear. The basic theory claims that the main structure is formed by boron and molybdenum. Zinc plays the role of a modifier, which only influences the structure without being part of it.

TEM images of 30MoO3–50ZnO–20B2O3 glassy sample

Margit Fabian, from the Hungarian Academy of Sciences, recently found evidence that contradicts this theory. In her study, supported by CERIC-ERIC, she used Neutron Diffraction, High Resolution Electron Microscopy and Solid- State Nuclear Magnetic Resonance together with computational simulation methods, to reveal the structure of several zinc-boromolybdate glasses with different compositions. The study not only produced precise structural data but also revealed that zinc plays an active role in forming the structure and is also fully incorporated. This new information is an important step towards a deeper understanding of this interesting class of materials and helps further to optimize the glasses for potential application.

  • Original article: M. Fabian, E. Svab, K. Krezhovc, Network structure with mixed bond-angle linkages in MoO3–ZnO–B2O3 glasses: Neutron diffraction and re- verse Monte Carlo modelling, Journal of Non-Crystalline Solids, Vol. 433, 2016, 6–13 (published online Nov. 2015)

Scientists change the morphology of graphene-like thin films for cheaper and environmentally friendly electronic devices*

Modern day electronics has high demand in organic opto-electronical materials for liquid-crystal displays, organic-LED and even organic photovoltaic elements. Such materials have to be transparent and conductive, as well as flexible, cheap and compatible with large scale manufacturing methods. Carbon based organic conductors, such as carbon-nanotubes and graphene thin-layers, are promising candidates for future organic opto-electronic devices. However, the production of carbon-based films having simultaneously high stability, controlled thickness and tunable properties is still a challenge.

(a) Images of the drop casted films corresponding to measured Samples A (pH 2.0), B (pH 3.7), C (pH 4.6), D (pH 9.5); (b) C 1s XPS spectrum on GL surface, and its deconvolution in Gaussian shape peaks corresponding to different functional groups.

Italian researchers around Michela Alfč and Valentina Gargiulo from IRC-CNR and the University of Naples have developed a new manufacturing process for graphene-like (GL) thin layers. Their process is performed in water and is therefore cheap, environmentally friendly and easy to scale for industrial production needs. In order to develop and improve the process further, a fundamental understanding of all aspects of the film preparation is crucial. In particular, the quality of the thin film is expected to be strongly dependent on the pH of the water suspension from which the films themselves are prepared. To obtain this understanding, the researchers used CERIC’s highly sensitive Synchrotron X-ray Photoelectron Spectroscopy (XPS) in combination with Atomic Force Microscopy (AFM) and Dynamic Light Scattering (DLS) to investigate the influence of the pH on the synthesis process. They found that the thin-layers consists of a film of carbon nanoparticles. The shape of these nanoparticles, as well as the thickness and morphology of the film, strongly depend on how acidic the reaction solution is. This information is a first but important step in understanding the physical mechanisms of the process and opens the way to the possibility of controlling the surface morphology of GL layers by properly acting on the preparation parameters.

  • Original article: M. Alfč et al., Applied Surface Science 353 (2015) 628–635, doi: 10.1016/j.apsusc.2015.06.117

New findings on the effects of impurities on catalytic combustion open the way to the production of cleaner energy*

The catalytic combustion of methane (CH4), the main component of natural gas, is a crucial process for the production of clean energy. Palladium (Pd)-based catalysts are the most active materials for the oxidation of methane at low temperatures. In contact with cerium oxide (CeO2), Pd reaches high activity. The synthesis of Pd nanoparticles surrounded by a thin porous shell of ceria allows full exploitation of this property. However, these catalysts can deactivate under real conditions, especially in the presence of water vapor, sulfur and phosphorus species, as seen in the irreversible deactivation of automotive catalytic converters. The presence of phosphorus compounds (P2O5 or H3PO4) in vehicle exhaust is due to decomposition/volatilization of anti-wear additives that are present in most available motor oils.

Matteo Monai (University of Trieste) and his colleagues shed some light into this matter by performing a fundamental investigation into the mechanism of phosphorous poisoning of catalysts*. The researchers prepared a model catalyst system and exposed it to phosphorous under various conditions. The behavior of the system was studied by a unique combination of techniques, some of which were offered by CERIC: Synchrotron Radiation Photoelectron Spectroscopy (XPS) Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM) and X-ray Absorption Near Edge Structure (XANES).

On the SEM image of the fresh catalyst (left) the surface appears smooth. After the aging experiment in the presence of water vapor and phosphorus (right image) CeO2 nanoparticles are clearly visible as white round dots.

The study led to the conclusion that phosphorous itself only lowers the performance of the catalyst, rather than destroying it completely. Only in combination with water vapor does it lead to the coagulation (clotting) of the CeO2 nanoparticles, which “lock-up” the palladium and completely deactivate the catalyst. An understanding of this mechanism can be used to design more stable catalytic systems, increasing the chance of tackling relevant environmental issues in the future.

  • Original article: M. Monai, et al., Phosphorus poisoning during wet oxidation of methane over Pd@CeO2/graphite model catalysts, published in Appl. Catal. B: Environ. (2015)

New design strategies towards more effective catalysts*

An efficient catalytic process is crucial for several applications, such as energy production in fuel cells and catalytic converters in cars. Precious noble-metals such as platinum play a key role in the catalysis and their use must be optimized to reduce costs and maximize their potential. Single-atom catalysts maximize the utilization of supported precious metals by exposing every single metal atom to reactants. Although this concept is widely known, preserving the stability of single atoms on a support material under working conditions (e.g. high temperature) is still a major challenge.

Filip Dvořák and Matteo Farnesi Camellone, with their colleagues from the Charles University in Prague, CNR-IOM DEMOCRITOS in Trieste and SISSA in Trieste, combined CERIC highly sensitive photoelectron spectroscopy with scanning tunneling microscopy and density functional theory calculations, to explore the physics and chemistry behind the exceptional activity of ceria-based catalysts with an atomic dispersion of ionic platinum.
Dvorak’s and Camellone’s study shows that monoatomic step-edges, which are the most pervasive defects on solid surfaces such as the support material ceria, provide specific structural and electronic environments for the selective formation of uniform, thermally and chemically stable Pt2+ ions. Moreover, they found that the platinum ions are stabilized as platinum oxide (PtO4), which can provide additional reactivity in oxidation reactions.

Location of the Platinum atoms (red) on the Ceria substrate. They were found adsorbed on the surface (a), replacing oxygen (b), as Pt6 cluster on the top of a monolayer (c) and, most stable, as PtO4 in the step-edge (d).

Experimentally controlling the engineering and decoration of the steps, as in the present study, may bring about a more effective use of precious metals in the catalytic processes, for less expensive and more environmentally friendly energy production.

  • Original article: Creating single-atom Pt-ceria catalysts by surface step decoration, published in Nature Communications, DOI:10.1038/ncomms10801

How nanoparticles give electrons away

Whether it is in catalytic processes in the chemical industry, environmental catalysis, new types of solar cells or new electronic components, nanoparticles are everywhere in modern production and environmental technologies, in which their unique properties ensure efficiency and save resources. The special properties of nanoparticles often arise from a chemical interaction with the support material on which they are placed. Such interactions often change the electronic structure of the nanoparticle because an electrical charge is exchanged between the particle and the support. Working groups led by Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and the University of Barcelona (UBCN) have now succeeded in counting the number of elementary charges that are lost by a platinum nanoparticle when it is placed onto a typical oxide support. Their work, realized thanks to access obtained through CERIC-ERIC and as part of the FP7 project chipCAT coordinated by the Director of the Czech CERIC-ERIC Partner Facility, Prof. Vladimir Matolin, brings the possibility of developing tailor-made nanoparticles a step closer.

Authors of graphics: Sergey Kozlov and Oriol Lamiel

Nanoscience has long investigated how nanoparticles interact with the support on which they are placed. It is now clear that various physical and chemical factors, such as the electronic structure, the nanostructure and – crucially – their interaction with the support, control the properties of nanoparticles. However, previous studies have not investigated how much charge is transferred and whether there is a relationship between the transfer and the size of the nanoparticle.

In order to measure the electrical charge that is exchanged,an international team of researchers from Germany, Spain, Italy and the Czech Republic, led by Prof. Dr. Jörg Libuda and Prof. Dr. Konstantin Neyman, prepared an extremely clean and atomically well-defined oxide surface, onto which they placed platinum nanoparticles. Using a highly sensitive detection method at the Czech Materials Science Beamline (MSB) in Elettra Sincrotrone Trieste, accessed through CERIC-ERIC call 1, the CERIC user Yaroslava Lykhach was able to quantify the effect for the first time. Looking at particles with various numbers of atoms, they counted the electrons transferred and showed that the effect is most pronounced for small nanoparticles with around 50 atoms. The magnitude of the effect is surprisingly large: approximately every tenth metal atom loses an electron when the particle is in contact with the oxide. The work involved a combination of multiple experimental techniques including CERIC-ERIC access time at microscopy and spectroscopy instruments of the Surface Physics Laboratory in Prague. The researchers were also able to use theoretical methods to show how the effect can be controlled, allowing the chemical properties to be adapted better to suit their intended application. This would allow valuable raw materials and energy to be used more efficiently in catalytic processes.

Publication's Reference

At the origin of cloud formation

Investigating aerosol nanoparticle dynamics with a multi-technique approach

Aerosol particles and clouds have a large net cooling effect on our planet and, according to the Intergovernmental Panel on Climate Change (IPCC), they represent the largest source of uncertainty in present climate models. Dr. Paul Winkler and PhD student Paulus Bauer, from the Faculty of Physics of the University of Vienna, have accessed CERIC facilities to shed new light on the very first steps of cloud formation, helping to improve understanding of the aerosol-cloud-climate connection.
Cloud droplets form on aerosol particles - tiny solid or liquid particles suspended in the atmosphere – above a size of about 50 nm. Aerosol particles are either directly emitted into the atmosphere (such as sea spray particles) or else form by the spontaneous clustering (“nucleation”) of trace atmospheric molecules. Around one half of cloud seeds are thought to originate from nucleated particles. However, the mechanisms of the gas-to-particle conversion are still poorly understood, as are the parameterizations of this process in climate models. Sulphuric acid is thought to play a key role but previous studies have shown that organic vapors also contribute to nanoparticle formation.
Winkler and Bauer have been studying this issue through the quantitative characterization of nanoparticle dynamics, with a focus on high time resolution.

The researchers accessed CERIC multiple complementary techniques to get direct information on particle size and number at sub-millisecond time-resolution and to study fundamental growth kinetics. Their project – nanoDynamite – funded by the European Research Council, is innovative in that it proposes the design of instruments that allow first in situ characterization of newly formed aerosol nanoparticles. The research into phase transition processes constitutes a vital link between molecular scale interactions and macroscopically relevant outcomes.

Thanks to the CERIC multi-technique open access service, the researchers have been able to develop their study through a new experimental approach, with the final goal of identifying and quantifying nanoparticle formation mechanisms. This will allow the prediction and utilization of macroscopic effects such as global-scale climatic impact caused by aerosol dynamics on the nanoscale.