Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral,fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra

Advances to the distributed, multi-core and fully cross-platform QuBiLS-MIDAS software v2.0 ( http://tomocomd.com/qubils-midas ) are reported in this article since the v1.0 release. The QuBiLS-MIDAS software is the only one that computes atom-pair and alignment-free geometrical MDs (3D-MDs) from several distance metrics other than the Euclidean distance, as well as alignment-free 3D-MDs that codify structural information regarding the relations among three and four atoms of a molecule. The most recent features added to the QuBiLS-MIDAS software v2.0 are related (a) to the calculation of atomic weightings from indices based on the vertex-degree invariant (e.g., Alikhanidi index); (b) to consider central chirality during the molecular encoding; (c) to use measures based on clustering methods and statistical functions to codify structural information among more than two atoms; (d) to the use of a novel method based on fuzzy membership functions to spherically truncate inter-atomic relations; and (e) to the use of weighted and fuzzy aggregation operators to compute global 3D-MDs according to the importance and/or interrelation of the atoms of a molecule during the molecular encoding. Moreover, a novel module to compute QuBiLS-MIDAS 3D-MDs from their headings was also developed. This module can be used either by the graphical user interface or by means of the software library. By using the library, both the predictive models built with the QuBiLS-MIDAS 3D-MDs and the QuBiLS-MIDAS 3D-MDs calculation can be embedded in other tools. A set of predefined QuBiLS-MIDAS 3D-MDs with high information content and low redundancy on a set comprised of 20,469 compounds is also provided to be employed in further cheminformatics tasks. This set of predefined 3D-MDs evidenced better performance than all the universe of Dragon (v5.5) and PaDEL 0D-to-3D MDs in variability studies, whereas a linear independence study proved that these QuBiLS-MIDAS 3D-MDs codify chemical information orthogonal to the Dragon 0D-to-3D MDs. This set of predefined 3D-MDs would be periodically updated as long as new results be achieved. In general, this report highlights our continued efforts to provide a better tool for a most suitable characterization of compounds, and in this way, to contribute to obtaining better outcomes in future applications.     

Color-Changing Sparks from Rare Earth Metal Powders

Commonly, sparks emit light according to the well-known black (gray) body radiation. Recently, we reported on color-changing sparks based on erbium powder, which switch their light emission between black body emission (surface combustion) and element-specific emission (vapor phase combustion). Herein, we investigated the spark formation from the adjacent rare-earth elements. The corresponding boiling points are significantly below (Yb, Sm, Tm) or above (Y, Lu) the boiling point of Er. While Yb and Sm evaporate too fast to form longer sparks, Y, Lu and Tm form color-changing sparks with varying length of the element-specific emission phase. The sparks were investigated by time-resolved emission spectroscopy, long-time exposures, and NIR/MIR imaging. The same basic pyrotechnic formulation containing one of these metal powders reveals a strongly differing burning behavior depending on the boiling point of the metal. The burning characteristics change from a green strobe (Yb) to intense colorful crackling (Tm) and finally a sparkling fountain with long-flying sparks (Lu, Y, Er).     

One-Pot Cooperation of Single-Atom Rh and Ru Solid Catalysts for a Selective Tandem Olefin Isomerization-Hydrosilylation Process

Realizing the full potential of oxide-supported single-atom metal catalysts (SACs) is key to successfully bridge the gap between the fields of homogeneous and heterogeneous catalysis. Here we show that the one-pot combination of Ru₁/CeO₂ and Rh₁/CeO₂ SACs enables a highly selective olefin isomerization-hydrosilylation tandem process, hitherto restricted to molecular catalysts in solution. Individually, monoatomic Ru and Rh sites show a remarkable reaction specificity for olefin double-bond migration and anti-Markovnikov α-olefin hydrosilylation, respectively. First-principles DFT calculations ascribe such selectivity to differences in the binding strength of the olefin substrate to the monoatomic metal centers. The single-pot cooperation of the two SACs allows the production of terminal organosilane compounds with high regio-selectivity (>95 %) even from industrially-relevant complex mixtures of terminal and internal olefins, alongside a straightforward catalyst recycling and reuse. These results demonstrate the significance of oxide-supported single-atom metal catalysts in tandem catalytic reactions, which are central for the intensification of chemical processes.     

Enantioselective Synthesis of a Tricyclic,sp3-Rich Diazatetradecanedione: an Amino Acid-Based Natural Product-Like Scaffold

6-, 7-, and 8-membered rings are assembled from a linear precursor by successive cyclisation reactions to construct a tricyclic diazatricyclo[6.5.1.0^{4, 9}]-tetradecanedione scaffold. Advanced building blocks based on d -aspartic acid and l -pyroglutamic acid were combined by a sp³−sp² Negishi coupling. A carbamate-guided syn-diastereoselective epoxidation followed by an intramolecular epoxide opening allowed the construction of the piperidine ring. An efficient one-pot hydroxyl-group protection twofold deprotection reaction prepared the ground for the cyclisation to the bicycle. A final deprotection of the orthogonal protecting groups and lactamisation led to the novel, sp³-rich tricycle. The final compound is a substrate mimic of peptidyl-prolyl cis-trans isomerases featuring a locked trans-amide bond. Cheminformatic analysis of 179 virtual derivatives indicates favourable physicochemical properties and drug-like characteristics. As proof of concept we, show a low micromolar activity in a fluorescence polarisation assay towards the FK506-binding protein 12.     

Improving the Switching Capacity of Glyco-Self-Assembled Monolayers on Au(111)

Self-assembled monolayers (SAMs) decorated with photoisomerizable azobenzene glycosides are useful tools for investigating the effect of ligand orientation on carbohydrate recognition. However, photoswitching of SAMs between two specific states is characterized by a limited capacity. The goal of this study is the improvement of photoswitchable azobenzene glyco-SAMs. Different concepts, in particular self-dilution and rigid biaryl backbones, have been investigated. The required SH-functionalized azobenzene glycoconjugates were synthesized through a modular approach, and the respective glyco-SAMs were fabricated on Au(111). Their photoswitching properties have been extensively investigated by applying a powerful set of methods (IRRAS, XPS, and NEXAFS). Indeed, the combination of tailor-made biaryl-azobenzene glycosides and suitable diluent molecules led to photoswitchable glyco-SAMs with a significantly enhanced and unprecedented switching capacity.     

Amino Acid Modified RNA Bases as Building Blocks of an Early Earth RNA-Peptide World

Fossils of extinct species allow us to reconstruct the process of Darwinian evolution that led to the species diversity we see on Earth today. The origin of the first functional molecules able to undergo molecular evolution and thus eventually able to create life, are largely unknown. The most prominent idea in the field posits that biology was preceded by an era of molecular evolution, in which RNA molecules encoded information and catalysed their own replication. This RNA world concept stands against other hypotheses, that argue for example that life may have begun with catalytic peptides and primitive metabolic cycles. The question whether RNA or peptides were first is addressed by the RNA-peptide world concept, which postulates a parallel existence of both molecular species. A plausible experimental model of how such an RNA-peptide world may have looked like, however, is absent. Here we report the synthesis and physicochemical evaluation of amino acid containing adenosine bases, which are closely related to molecules that are found today in the anticodon stem-loop of tRNAs from all three kingdoms of life. We show that these adenosines lose their base pairing properties, which allow them to equip RNA with amino acids independent of the sequence context. As such we may consider them to be living molecular fossils of an extinct molecular RNA-peptide world.     

Pandemic-Driven Development of a Medical-Grade,Economic and Decentralized Applicable Polyolefin Filament for Additive Fused Filament Fabrication

A polyolefin with certified biocompatibility according to USP class VI was used by our group as feedstock for filament-based 3D printing to meet the highest medical standards in order to print personal protective equipment for our university hospital during the ongoing pandemic. Besides the chemical resistance and durability, as well as the ability to withstand steam sterilization, this polypropylene (PP) copolymer is characterized by its high purity, as achieved by highly efficient and selective catalytic polymerization. As the PP copolymer is suited to be printed with all common printers in fused filament fabrication (FFF), it offers an eco-friendly cost–benefit ratio, even for large-scale production. In addition, a digital workflow was established focusing on common desktop FFF printers in the medical sector. It comprises the simulation-based optimization of personalized print objects, considering the inherent material properties such as warping tendency, through to validation of the process chain by 3D scanning, sterilization, and biocompatibility analysis of the printed part. This combination of digital data processing and 3D printing with a sustainable and medically certified material showed great promise in establishing decentralized additive manufacturing in everyday hospital life to meet peaks in demand, supply bottlenecks, and enhanced personalized patient treatment.     

Gadolinium Photocatalysis: Dearomative [2+2] Cycloaddition/Ring‐Expansion Sequence with Indoles

Lanthanide photocatalysts are much less investigated in synthetic chemistry than rare and expensive late transition metals. We herein introduce Gd^III photocatalysis of a highly regioselective, intermolecular [2+2] photocycloaddition/ring‐expansion sequence with indoles, which could provide divergent access to cyclopenta[b]indoles and indolines. A simple and commercially available Gd(OTf)₃ salt is sufficient for this visible‐violet‐light‐induced transformation. The reaction proceeds either through a transient or start‐to‐end dearomatization cascade and shows excellent regioselectivity (usually >95:5 r.r.), broad scope (59 examples), good functional group tolerance and facile scale‐up under mild, direct visible‐light‐excitation conditions. Mechanistic investigations reveal that direct excitation of the Gd(OTf)₃/indole mixture gives an excited state intermediate, which undergoes the subsequent [2+2] cycloaddition and cyclobutane‐expansion cascade.     

Transition‐Metal‐Functionalized DNA Double‐Crossover Tiles: Enhanced Stability and Chirality Transfer to Metal Centers

The double crossover junction (DX) is a fundamental building block for generating complex and varied structures from DNA. However, its implementation in functional devices is limited to the inherent properties of DNA itself. Here, we developed design strategies to generate the first metal–DX DNA tiles (DX_M) by site‐specifically functionalizing the tile crossovers with tetrahedral binding pockets that coordinate Cu^I. These DX junctions bind two Cu^I ions independently at distinct sites, display greater thermal stability than native DX tiles upon metalation, and melt in a cooperative fashion. In addition, the right‐handed helical chirality of DNA is transferred to the metal centers. Our tiles display high metal ion selectivity, such that Cu^II is spontaneously reduced to Cu^I in situ. By modifying our design over three generations of tiles, we elucidated the thermodynamic and geometric requirements for the successful assembly of DX_M tiles, which have direct applicability in developing robust, stable DNA‐based materials with electroactive, photoactive, and catalytic properties.     

One‐Pot Cooperation of Single‐Atom Rh and Ru Solid Catalysts for a Selective Tandem Olefin Isomerization‐Hydrosilylation Process

Realizing the full potential of oxide‐supported single‐atom metal catalysts (SACs) is key to successfully bridge the gap between the fields of homogeneous and heterogeneous catalysis. Here we show that the one‐pot combination of Ru₁/CeO₂ and Rh₁/CeO₂ SACs enables a highly selective olefin isomerization‐hydrosilylation tandem process, hitherto restricted to molecular catalysts in solution. Individually, monoatomic Ru and Rh sites show a remarkable reaction specificity for olefin double‐bond migration and anti‐Markovnikov α‐olefin hydrosilylation, respectively. First‐principles DFT calculations ascribe such selectivity to differences in the binding strength of the olefin substrate to the monoatomic metal centers. The single‐pot cooperation of the two SACs allows the production of terminal organosilane compounds with high regio‐selectivity (>95 %) even from industrially‐relevant complex mixtures of terminal and internal olefins, alongside a straightforward catalyst recycling and reuse. These results demonstrate the significance of oxide‐supported single‐atom metal catalysts in tandem catalytic reactions, which are central for the intensification of chemical processes.