The photon-ion merged-beams experiment PIPE at PETRA III—The first five years

The Photon-Ion Spectrometer at PETRA III—in short, PIPE—is a permanently installed user facility at the "Variable Polarization XUV Beamline" P04 of the synchrotron light source PETRA III operated by DESY in Hamburg, Germany. The careful design of the PIPE ion-optics in combination with the record-high photon flux at P04 has lead to a breakthrough in experimental studies of photon interactions with ionized small quantum systems. This short review provides an overview over the published scientific results from photon-ion merged-beams experiments at PIPE that were obtained since the start of P04 operations in 2013. The topics covered comprise photoionization of ions of astrophysical relevance, quantitative studies of multi-electron processes upon inner-shell photoexcitation and photoionization of negative and positive atomic ions, precision spectroscopy of photoionization resonances, photoionization and photofragmentation of molecular ions, and of endohedral fullerene ions.     

Interaction of PiB‐Derivative Metal Complexes with Beta‐Amyloid Peptides: Selective Recognition of the Aggregated Forms

Metal complexes are increasingly explored as imaging probes in amyloid peptide related pathologies. We report the first detailed study on the mechanism of interaction between a metal complex and both the monomer and the aggregated form of Aβ_1–40 peptide. We have studied lanthanide(III) chelates of two PiB‐derivative ligands (PiB=Pittsburgh compound B), L¹ and L², differing in the length of the spacer between the metal‐complexing DO3A macrocycle (DO3A= 1,4,7,10‐tetraazacyclododecane‐1,4,7‐triacetic acid) and the peptide‐recognition PiB moiety. Surface plasmon resonance (SPR) and saturation transfer difference (STD) NMR spectroscopy revealed that they both bind to aggregated Aβ_1–40 (K_D=67–160 μM ), primarily through the benzothiazole unit. HSQC NMR spectroscopy on the ¹⁵N‐labeled, monomer Aβ_1–40 peptide indicates nonsignificant interaction with monomeric Aβ. Time‐dependent circular dichroism (CD), dynamic light scattering (DLS), and TEM investigations of the secondary structure and of the aggregation of Aβ_1–40 in the presence of increasing amounts of the metal complexes provide coherent data showing that, despite their structural similarity, the two complexes affect Aβ fibril formation distinctly. Whereas GdL¹, at higher concentrations, stabilizes β‐sheets, GdL² prevents aggregation by promoting α‐helical structures. These results give insight into the behavior of amyloid‐targeted metal complexes in general and contribute to a more rational design of metal‐based diagnostic and therapeutic agents for amyloid‐ associated pathologies.     

1H NMR studies of binary and ternary dapsone supramolecular complexes with different drug carriers: EPC liposome,SBE‐β‐CD and β‐CD

Binary and ternary systems composed of dapsone, sulfobutylether‐β‐cyclodextrin (SBE‐β‐CD), β‐CD and egg phosphatidylcholine (EPC) were evaluated using 1D ROESY, saturation transfer difference NMR and diffusion experiments (DOSY) revealing the binary complexes Dap/β‐CD (K_a 1396 l mol^?1), Dap/SBE‐β‐CD (K_a 246 l mol^?1), Dap/EPC (K_a 84 l mol^?1) and the ternary complex Dap/β‐CD/EPC (K_a 18 l mol^?1) in which dapsone is more soluble. Copyright © 2014 John Wiley & Sons, Ltd.     

A comparative study using conventional methods,ionic liquids,microwave irradiation and combinations thereof for the synthesis of 5-trifluoroacetyl-1,2,3,4-tetrahydropyridines

This study reports a comparison between conventional methods, ionic liquids, microwave (MW) irradiation, and combinations thereof for the synthesis of a series of fourteen 1-aryl-2-arylamino-5-trifluoroacetyl-1,2,3,4-tetrahydropyridines. In all of the reactions tested, the products were obtained at very good yields (87–97%), but the reaction times were very different, depending on the method used. Comparing to other methods, the time decreased to 1?min when [BMIM]BF₄ under MW irradiation was used, thus evidencing a synergic effect.     

Touching proteins with virtual bare hands

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more accessible and intuitive visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). While bespoke commercial VR suites are available, in this work, we present a freely available software pipeline for visualising protein structures through VR. New consumer hardware, such as the HTC Vive and the Oculus Rift utilized in this study, are available at reasonable prices. As an instructive example, we have combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-led drug design by exposing molecular interactions that might be hidden in the less informative static models. This is a paradigmatic test case scenario for many similar applications in computer-aided molecular studies and design.     

Self-assembled films based on polypyrrole and carbon nanotubes composites for the determination of Diuron pesticide

In this work, polypyrrole (PPy) and its respective composite with functionalized multi-walled carbon nanotubes (MWCNT) were obtained by chemical polymerization of the monomer pyrrole in aqueous solution. The obtained PPy as well as its composite (PPy-MWCNT) were characterized by Fourier transform infrared spectroscopy (FTIR) and were used to produce nanostructured self-assembled (SA) films deposited onto glass substrates covered with indium tin oxide (ITO). The SA films were produced with alternated layers of polystyrene sulphonated (PSS) and were characterized by UV-visible, cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and scanning electron microscopy (SEM) analyses. The applicability of the SA films was evaluated by square wave voltammetry (SWV) with standard additions of aliquots of Diuron pesticide in Britton-Robinson buffer solutions (pH = 2.0). The results showed an oxidation peak at 0.23 V which increases in function of the Diuron concentration for both the SA films. It was also observed that the SA film based on the composite (PPy-MWCNT/PSS) showed a peak current intensity about ten times higher in comparison with its unmodified counterpart (PPy/PSS) for a Diuron concentration of 4.29 × 10^?5 mol L^?1, indicating a synergic effect between PPy and MWCNT in the composite. The limits of quantification (LOQ) and limits of detection (LOD) were respectively 8.6 × 10^?7 mol L^?1 and 2.6 × 10^?7 mol L^?1.