Practical aspects of electron energy-loss spectroscopy (EELS) calculations using FEFF8

We discuss the application of the ab initio program FEFF8 to calculations of electron energy-loss spectroscopy (EELS), focusing in particular on core-loss spectra. FEFF8 is based on a self-consistent, real space multiple scattering formalism. We focus on issues relevant to practical simulations, including the construction of well-converged potentials, the treatment of inelastic losses and exchange-correlation potentials and the core-hole. We also discuss how to account for experimental conditions, for example, sample orientation and finite temperature effects such as Debye-Waller factors. Finally we discuss the interpretation of the spectra in terms of electronic structure and local projected density of states (LDOS). As an explicit example, we illustrate various features of the code by application to the ionization edges of GaN.     

Heterocyclic compounds as antiviral drugs: Synthesis,structure–activity relationship and traditional applications

A virus outbreak challenges the economic, medical, and public health infrastructure worldwide. More than one virus capable of triggering diseases have been identified per year since 1972, which requires the development of new ways of treatment and prevention, however, such processes are not rapid and easy. With the pandemic scenario experienced since early 2020, several drugs with well-known purposes have gained prominence, due to speculation of their use in the treatment against the new coronavirus. Among the main drugs studied, the vast majority contain a heterocyclic structure. In this review, we presented the traditional and efficient synthesis of 15 drugs that have been studied for the COVID-19 treatment, containing in their structure heterocycles like indole, quinoline, pyrimidone, tetrahydrofuran, pyrrolidine, triazole, pyridazine, pyrazole, pyrrolopyrimidine, azetidine, pyrrolotriazine, pyrazine, tetrahydropyran, benzofuran, spiroketal, and thiazole. Furthermore, we have shown the original applications, as well as their structure–activity relationship and what is their situation as a drug candidate against COVID-19. Thus, the objective was to consolidate the main synthetic and pharmacological aspects involving clinically developed heterocycles that at some point were presented as promising against SARS-CoV-2.     

New Ideas for Understanding the Structure and Magnetism in AgF2: Prediction of Ferroelasticity

In the search for new high-temperature superconductors, it has been proposed that there are strong similarities between the fluoroargentate AgF₂ and the cuprate La₂CuO₄. We explored the origin of the possible layered structure of AgF₂ by studying its parent high-symmetry phase and comparing these results with those of a seemingly analogous cuprate, CuF₂. Our findings first stress the large differences between CuF₂ and AgF₂. Indeed, the parent structure of AgF₂ is found to be cubic, naturally devoid of any layering, even though Ag²⁺ ions occupy trigonal sites that, nevertheless, allow the existence of a Jahn-Teller effect. The observed Pbca orthorhombic phase is found when the system is cooperatively distorted by a local E⊗e trigonal Jahn-Teller effect around the silver sites that creates both geometrical and magnetic layering. While the distortion implies that two Ag²⁺−F⁻ bonds increase their distance by 15 % and become softer, our simulations indicate that covalent bonding and interlayer electron hopping is strong, unlike the situation in cuprate superconductors, and that, in fact, exfoliation of individual planes might be a harder task than previously suggested. As a salient feature, these results prove that the actual magnetic structure in AgF₂ is a direct consequence of vibronic contributions involved in the Jahn-Teller effect. Finally, our findings show that, due to the multiple minima intrinsic to the Jahn-Teller energy surface, the system is ferroelastic, a property that is strongly coupled to magnetism in this argentate.     

The Photophysics and Photochemistry of Melanin- Like Nanomaterials Depend on Morphology and Structure

Melanin-like nanomaterials have found application in a large variety of high economic and social impact fields as medicine, energy conversion and storage, photothermal catalysis and environmental remediation. These materials have been used mostly for their optical and electronic properties, but also for their high biocompatibility and simplicity and versatility of preparation. Beside this, their chemistry is complex and it yields structures with different molecular weight and composition ranging from oligomers, to polymers as well as nanoparticles (NP). The comprehension of the correlation of the different compositions and morphologies to the optical properties of melanin is still incomplete and challenging, even if it is fundamental also from a technological point of view. In this minireview we focus on scientific papers, mostly recent ones, that indeed examine the link between composition and structural feature and photophysical and photochemical properties proposing this approach as a general one for future research.     

Optimized IR synchrotron beamline design

Synchrotron infrared beamlines are powerful tools on which to perform spectroscopy on microscopic length scales but require working with large bending‐magnet source apertures in order to provide intense photon beams to the experiments. Many infrared beamlines use a single toroidal‐shaped mirror to focus the source emission which generates, for large apertures, beams with significant geometrical aberrations resulting from the shape of the source and the beamline optics. In this paper, an optical layout optimized for synchrotron infrared beamlines, that removes almost totally the geometrical aberrations of the source, is presented and analyzed. This layout is already operational on the IR beamline of the Brazilian synchrotron. An infrared beamline design based on a SOLEIL bending‐magnet source is given as an example, which could be useful for future IR beamline improvements at this facility.     

Ab Initio Study on the Stability of NgnBe2N2, NgnBe3N2 and NgBeSiN2 Clusters

The global minima of Be₂N₂, Be₃N₂ and BeSiN₂ clusters are identified using a modified stochastic kick methodology. The structure, stability and bonding nature of these clusters bound to noble gas (Ng) atoms are studied at the MP2/def2‐QZVPPD level of theory. Positive Be?Ng bond dissociation energy, which gradually increases down Group 18 from He to Rn, indicates the bound nature of Ng atoms. All of the Ng‐binding processes are exothermic in nature. The Xe and Rn binding to Be₂N₂ and Be₃N₂ clusters and Ar?Rn binding to BeSiN₂ are exergonic processes at room temperature; however, for the lighter Ng atoms, lower temperatures are needed. Natural population analysis, Wiberg bond index computations, electron density analysis, and energy decomposition analysis are performed to better understand the nature of Be?Ng bonds.     

Structural Insights into the Design of Synthetic Nanobody Libraries

Single domain antibodies from camelids, or nanobodies, are a unique class of antibody fragments with several advantageous characteristics: small monomeric size, high stability and solubility and easy tailoring for multiple applications. Nanobodies are gaining increasing acceptance as diagnostic tools and promising therapeutic agents in cancer and other diseases. While most nanobodies are obtained from immunized animals of the camelid family, a few synthetic nanobody libraries constructed in recent years have shown the capability of generating high quality nanobodies in terms of affinity and stability. Since this synthetic approach has important advantages over the use of animals, the recent advances are indeed encouraging. Here we review over a dozen synthetic nanobody libraries reported so far and discuss the different approaches followed in their construction and validation, with an emphasis on framework and hypervariable loop design as critical issues defining their potential as high-class nanobody sources.     

Production and Digestibility Studies of β-Galactosyl Xylitol Derivatives Using Heterogeneous Catalysts of LacA β-Galactosidase from Lactobacillus Plantarum WCFS1

The synthesis of β-galactosyl xylitol derivatives using immobilized LacA β-galactosidase from Lactobacillus plantarum WCFS1 is presented. These compounds have the potential to replace traditional sugars by their properties as sweetener and taking the advantages of a low digestibility. The enzyme was immobilized on different supports, obtaining immobilized preparations with different activity and stability. The immobilization on agarose-IDA-Zn-CHO in the presence of galactose allowed for the conserving of 78% of the offered activity. This preparation was 3.8 times more stable than soluble. Since the enzyme has polyhistidine tags, this support allowed the immobilization, purification and stabilization in one step. The immobilized preparation was used in synthesis obtaining two main products and a total of around 68 g/L of β-galactosyl xylitol derivatives and improving the synthesis/hydrolysis ratio by around 30% compared to that of the soluble enzyme. The catalyst was recycled 10 times, preserving an activity higher than 50%. The in vitro intestinal digestibility of the main β-galactosyl xylitol derivatives was lower than that of lactose, being around 6 and 15% for the galacto-xylitol derivatives compared to 55% of lactose after 120 min of digestion. The optimal amount immobilized constitutes a very useful tool to synthetize β-galactosyl xylitol derivatives since it can be used as a catalyst with high yield and being recycled for at least 10 more cycles.