Surface chemistry of silicon nanoclusters

We employ density functional and quantum Monte Carlo calculations to show that significant changes occur in the gap of fully hydrogenated nanoclusters when the surface contains passivants other than hydrogen, in particular atomic oxygen. In the case of oxygen, the gap reduction computed as a function of the nanocluster size provides a consistent interpretation of several recent experiments. Furthermore, we predict that other double bonded groups also significantly affect the optical gap, while single bonded groups have a minimal influence.     

Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins

In the present work a data analysis approach, based on XAFS data, is proposed for the identification of most probable binding motifs of unknown mononuclear zinc sites in metalloproteins. This approach combines multiple‐scattering EXAFS analysis performed within the rigid‐body refinement scheme, non‐muffin‐tin ab initio XANES simulations, average structural information on amino acids and metal binding clusters provided by the Protein Data Bank, and Debye–Waller factor calculations based on density functional theory. The efficiency of the method is tested by using three reference zinc proteins for which the local structure around the metal is already known from protein crystallography. To show the applicability of the present analysis to structures not deposited in the Protein Data Bank, the XAFS spectra of six mononuclear zinc binding sites present in diverse membrane proteins, for which we have previously proposed the coordinating amino acids by applying a similar approach, is also reported. By comparing the Zn K‐edge XAFS features exhibited by these proteins with those pertaining to the reference structures, key spectral characteristics, related to specific binding motifs, are observed. These case studies exemplify the combined data analysis proposed and further support its validity.     

Non-invasive characterisation of SIX Japanese hand-guards (tsuba)

In this work we present a systematic study of Japanese sword hand-guards (tsuba) carried out by means of non-invasive techniques using neutrons. Several tsuba from different periods, belonging to the Japanese Section of the Stibbert Museum, were analysed using an innovative approach to characterise the bulk of the samples, coupling two neutron techniques, namely Time of Flight Neutron Diffraction (ToF-ND) and Nuclear Resonance Capture Analysis (NRCA). The measurements were carried out on the same instrument: the INES beam-line at the ISIS spallation pulsed neutron source (UK). NRCA analysis allows identifying the elements present in the sample gauge volume, while neutron diffraction is exploited to quantify the phase distribution and other micro-structural parameters of the metal specimen. The results show that all samples are made of high-quality metal, either steel or copper alloy, with noticeable changes in composition and working techniques, depending on the place and time of manufacturing.     

Atomic control of water interaction with biocompatible surfaces: the case of SiC(001)

The interaction of water with Si- and C- terminated beta-SiC(001) surfaces was investigated by means of ab initio molecular dynamics simulations. Irrespective of coverage, varied from 1/4 to 1 monolayer, we found that water dissociates on the Si-terminated surface, substantially modifying the clean surface reconstruction, while the C-terminated surface is nonreactive and hydrophobic. Based on our results, we propose that STM images and photoemission experiments may detect specific changes induced by water on both the structural and electronic properties of SiC(001) surfaces.     

First principles and classical molecular dynamics simulations of solvated benzene

We have performed extensive ab initio and classical molecular dynamics (MD) simulations of benzene in water in order to examine the unique solvation structures that are formed. Qualitative differences between classical and ab initio MD simulations are found and the importance of various technical simulation parameters is examined. Our comparison indicates that nonpolarizable classical models are not capable of describing the solute-water interface correctly if local interactions become energetically comparable to water hydrogen bonds. In addition, a comparison is made between a rigid water model and fully flexible water within ab initio MD simulations which shows that both models agree qualitatively for this challenging system.     

Structure and dynamics of a partially folded protein are decoupled from its mechanism of aggregation

A common strategy to study the mechanism of amyloid formation is the characterization of the structure and dynamics of the precursor state, which is in most cases a partially folded protein. Here we investigated the highly dynamic conformational state formed by the protein domain HypF-N at low pH, before aggregation, using fluorescence, circular dichroism, and NMR spectroscopies. The NMR analysis allowed us, in particular, to identify the regions of the sequence that form hydrophobic interactions and adopt an alpha-helical secondary structure in the pH-denatured ensemble. To understand the role that this residual structure plays in the aggregation of this protein, we probed the mechanism of aggregation using protein engineering experiments and thus identified the regions of the sequence of HypF-N that play a critical role in the conversion of this dynamic state into thioflavin T-binding and beta-sheet containing protofibrils. The combination of these two complementary approaches revealed that the aggregation of pH-denatured HypF-N is not structure-dependent, meaning that it is not driven by the regions of the protein that are either less or more protected in the initial partially folded state. It is, by contrast, promoted by discrete protein regions that have the highest intrinsic propensity to aggregate because of their physicochemical properties.     

Hydrogen Peroxide Detection Using Prussian Blue-modified 3D Pyrolytic Carbon Microelectrodes

A highly sensitive amperometric Prussian blue-based hydrogen peroxide sensor was developed using 3D pyrolytic carbon microelectrodes. A 3D printed multielectrode electrochemical cell enabled simultaneous highly reproducible Prussian blue modification on multiple carbon electrodes. The effect of oxygen plasma pre-treatment and deposition time on Prussian blue electrodeposition was studied. The amperometric response of 2D and 3D sensors to the addition of hydrogen peroxide in μM and sub-μM concentrations in phosphate buffer was investigated. A high sensitivity comparable to flow injection systems and a detection limit of 0.16 μM was demonstrated with 3D pyrolytic carbon microelectrodes at stirred batch condition