Crystal Structure and Local Dynamics in Tetrahedral Proton-Conducting La1-xBa1+xGaO4

La1-xBa1+xGaO4-0 (LBG) compounds, based on unconnected GaO4 moieties, were recently proposed as proton conductors. Protonic defects in the lattice are inserted through self-doping with Ba2+, to create oxygen vacancies subsequently filled by hydroxyl ions. We present a combined structural analysis on self-doped LBG using X-ray diffraction (XRD) and X-ray absorption (EXAFS): these results unravel the finer structural details on the short-range and long-range scales, and they are correlated with the dynamical properties of protonic conduction coming from vibrational spectroscopy. The structure of the GaO4 groups is independent of the oxide composition. On hydration, an array of short intertetrahedral hydrogen bonds is formed, producing a contraction of the a axis. On the basis of thermogravimetric analysis, EXAFS, XRD and infrared spectroscopy (IR) results, we propose that the stiffness of the GaO4 tetrahedra hinders the intratetrahedral proton transfer, while the noticeable fraction of protons involved in strong hydrogen bonds limit the proton reorientational freedom

Dopants and defects in proton-conducting perovskites

Many doped perovskites show high proton conductivity at intermediate to high temperatures (500- 900 °C), which has opened possibilities for many prospected applications in energy conversion (fuel cells), and electrochemical devices. In a doped perovskite, e.g. BaCe1-xYxO3-y, oxygen vacancies are created by charge compensation, and can eventually react with air moisture to form structural protonic defects. The sluggish nature of the proton, which is practically invisible to most structural analyses, and poses enormous problems to quantum chemistry, has surely contributed to slow down the progress in the understanding of these materials: in fact, the conduction dynamics and its interplay with structure are still matter of debate. The kind of trivalent dopant and its size, and the doping level, have all been found to critically influence the conductivity: to date, however, no comprehensive model was developed, and no clear explanations exist between the chemical and dynamical properties. Here we present results collected in several EXAFS experiments on doped BaCeO3 and BaZrO3 spanning three years, on the Ba site, Ce site, and the dopant (yttrium, gadolinium, indium: the ionic sizes of these are respectively equal, larger and smaller than Ce4+) site. The local structures up to about 6 Å around each site are solved with state-of-the-art techniques employing both the GNXAS and FEFF approaches, revealing unique features and demonstrating that in this case the conventional diffraction techniques are not suited to unravel the complexity of doped crystals. In particular, the attention will be drawn on the local deviations from Vegard’s law, the local expansion/contraction as a function of hydration degree, the interplay between dopant and defects, and the chemical compatibility (Pearson absolute hardness) instead of ionic size matching. The EXAFS results are correlated with complementary information about the dynamics of protons and other defects (IR and neutron vibrational spectroscopy, QENS, ionic and electronic conductivity measurements)

Indium doping of proton-conducting solid oxides

Solid oxides protonic conductors are prepared by doping the pure matrix compounds with cationic species. Barium cerate and barium zirconate are perovskite-like compounds, characterized by a network of corner-sharing MeO6 octahedra (Me=Ce, Zr). Barium lies in the cavities between octahedra. Insertion of trivalent species in the octahedral site involves the formation of charge- compensating oxygen vacancies, that can be filled by hydroxyls coming from dissociative water absorption. Then, proton delocalization among structural oxygens ensures conductivity. The most effective conductors are obtained by yttrium doping that, on the other hand, enters only in limited amounts in both BaZrO3 and BaCeO3, thus involving limited carrier concentration. Perovskites are affected by different drawbacks: barium cerate compounds are very sensitive to the acidic components present in the environment and in particular to CO2 that induces decomposition in barium carbonate and cerium oxide; barium zirconate, notwithstanding a very high bulk conductivity, is biased by high grain boundary resistivity. A possible alternative to perovskite-like compounds is constituted by fergusonite-type lanthanum niobate and lanthanum tantalate compounds, characterized by a tetrahedral coordination of Nb and Ta. These oxides present a very high chemical stability but very low carrier concentration, usually induced by Ca-doping the lanthanum site [1]. Among the different trivalent dopants, it was demonstrated by X-ray absorption spectroscopy that indium is able to enter in any composition in the perovskite network, thus providing a very high carrier concentration, even if with lower proton mobility. This property of indium was ascribed to its electronic structure and in particular to the low Pearson hardness, allowing this cation to fit in a hosting matrix with the least structural strain [2]. A preliminar attempt of exploiting indium for enhancing the carrier concentration of lanthanum niobate was carried out. The solid state synthesis involved amounts of the reactant simple oxides suitable to force indium doping of the niobium site. X-ray diffraction do not show significant amounts of secondary oxide phases

Pharmacophore modelling as useful tool in the lead compounds identification and optimization

The goal of computer-aided molecular design methods in modern medicinal chemistry is to reduce the overall cost and time associated to the discovery and development of a new drug by identifying the most promising candidates to focus the experimental efforts on. Very often, many drug discovery projects have reached already a well-advanced stage before detailed structural data on the protein target have become available. A possible consequence is that often, medicinal chemists develop novel compounds for a target using preliminary structure–activity information, together with the theoretical models of interactions. Only responses that are consistent with the working hypothesis contribute to an evolution of the used models. Within this framework, the pharmacophore approach has proven to be successful, allowing the perception and understanding of key interactions between a receptor and a ligand[1]. In recent years, our research group exploited this useful modeling tool with the aim to identify new chemical entities and/or optimizing known lead compounds to obtain more active drugs in the field of antitumor, antiviral, and antibacterial drugs. In this communication, we present an overview of our recent works in which we used the pharmacophore modelling approach combined with induced fit docking, 3D-QSAR approach, and HTVS for the analysis of drug-receptor interactions and the discovery of new inhibitors of IKKβ, Bcl-xl, and c-kit tyrosine kinase, all targets involved into the initiation and the development of different types of cancer[2-5]

Scaffold-Hopping Strategies in Aurone Optimization: A Comprehensive Review of Synthetic Procedures and Biological Activities of Nitrogen and Sulfur Analogues

: Aurones, particular polyphenolic compounds belonging to the class of minor flavonoids and overlooked for a long time, have gained significative attention in medicinal chemistry in recent years. Indeed, considering their unique and outstanding biological properties, they stand out as an intriguing reservoir of new potential lead compounds in the drug discovery context. Nevertheless, several physicochemical, pharmacokinetic, and pharmacodynamic (P3) issues hinder their progression in more advanced phases of the drug discovery pipeline, making lead optimization campaigns necessary. In this context, scaffold hopping has proven to be a valuable approach in the optimization of natural products. This review provides a comprehensive and updated picture of the scaffold-hopping approaches directed at the optimization of natural and synthetic aurones. In the literature analysis, a particular focus is given to nitrogen and sulfur analogues. For each class presented, general synthetic procedures are summarized, highlighting the key advantages and potential issues. Furthermore, the biological activities of the most representative scaffold-hopped compounds are presented, emphasizing the improvements achieved and the potential for further optimization compared to the aurone class

Bioisosteric heterocyclic analogues of natural bioactive flavonoids by scaffold-hopping approaches: State-of-the-art and perspectives in medicinal chemistry

: The flavonoid family is a set of well-known bioactive natural molecules, with a wide range of potential therapeutic applications. Despite the promising results obtained in preliminary in vitro/vivo studies, their pharmacokinetic and pharmacodynamic profiles are severely compromised by chemical instability. To address this issue, the scaffold-hopping approach is a promising strategy for the structural optimization of natural leads to discover more potent analogues. In this scenario, this Perspective provides a critical analysis on how the replacement of the chromon-4-one flavonoid core with other bioisosteric nitrogen/sulphur heterocycles might affect the chemical, pharmaceutical and biological properties of the resulting new chemical entities. The investigated derivatives were classified on the basis of their biological activity and potential therapeutic indications. For each session, the target(s), the specific mechanism of action, if available, and the key pharmacophoric moieties were highlighted, as revealed by X-ray crystal structures and in silico structure-based studies. Biological activity data, in vitro/vivo studies, were examined: a particular focus was given on the improvements observed with the new heterocyclic analogues compared to the natural flavonoids. This overview of the scaffold-hopping advantages in flavonoid compounds is of great interest to the medicinal chemistry community to better exploit the vast potential of these natural molecules and to identify new bioactive molecules

Long-Range and Short-Range Structure of Proton-Conducting Y:BaZrO3

Yttrium-doped barium zirconate (BZY) is the most promising candidate for proton-conducting ceramics and has been extensively studied in recent years. The detailed features of the crystal structure, both short-range and long-range, as well as the crystal chemistry driving the doping process, are largely unknown. We use very high resolution X-ray diffraction (HR-XRD) to resolve the crystal structure, which is very slightly tetragonally distorted in BZY, while the local environment around Zr4+ and Y3+ is probed with extended X-ray absorption fine structure (EXAFS), and the symmetry and vibrations are investigated by using Raman spectroscopy. It is found that barium zirconate shows some degree of local deviation from the cubic arystotype even if undoped, which upon substitution by the perceptibly larger Y3+, playing the role of a rigid inclusion, is further increased. This distortion is one limiting factor concerning the Y3+ solubility. The effects are correlated to the proton conduction properties of BZY

DRUDIT: web-based DRUgs DIscovery Tools to design small molecules as modulators of biological targets.

Abstract Motivation New in silico tools to predict biological affinities for input structures are presented. The tools are implemented in the DRUDIT (DRUgs DIscovery Tools) web service. The DRUDIT biological finder module is based on molecular descriptors that are calculated by the MOLDESTO (MOLecular DEScriptors TOol) software module developed by the same authors, which is able to calculate more than one thousand molecular descriptors. At this stage, DRUDIT includes 250 biological targets, but new external targets can be added. This feature extends the application scope of DRUDIT to several fields. Moreover, two more functions are implemented: the multi- and on/off-target tasks. These tools applied to input structures allow for predicting the polypharmacology and evaluating the collateral effects. Results The applications described in the article show that DRUDIT is able to predict a single biological target, to identify similarities among biological targets, and to discriminate different target isoforms. The main advantages of DRUDIT for the scientific community lie in its ease of use by worldwide scientists and the possibility to be used also without specific, and often expensive, hardware and software. In fact, it is fully accessible through the WWW from any device to perform calculations. Just a click or a tap can start tasks to predict biological properties for new compounds or repurpose drugs, lead compounds, or unsuccessful compounds. To date, DRUDIT is supported by four servers each able to execute 8 jobs simultaneously. Availability and implementation The web service is accessible at the www.drudit.com URL and its use is free of charge. Supplementary information Supplementary data are available at Bioinformatics online