Synthesis and Surface‐Spectroscopic Characterization of Photoisomerizable glyco‐SAMs on Au(111)

Photoisomerizable glyco‐SAMs (self‐assembled monolayers), utilizing synthetic azobenzene glycoside derivatives were fabricated. The ultimate goal of this project is to assay the influence of the 3D arrangement of sugar ligands on cell adhesion, and eventually make cell adhesion photoswitchable. However, it is a prerequisite for any biological study on the spatial conditions of carbohydrate recognition, that photoisomerization of the surface molecules can be verified. Here, we employed IRRAS and XPS to spectroscopically characterize glyco‐SAMs. In particular and unprecedented to date, we prove reversible E→Z→E isomerization of azobenzene glycoside‐terminated SAMs.     

Experimental and Computational Studies of a Multi‐Electron Donor–Acceptor Ligand Containing the Thiazolo[5,4‐d]thiazole Core and its Incorporation into a Metal–Organic Framework

A ligand containing the thiazolo[5,4‐d]thiazole (TzTz) core (acceptor) with terminal triarylamine moieties (donors), N,N′‐(thiazolo[5,4‐d]thiazole‐2,5‐diylbis(4,1‐phenylene))bis(N‐(pyridine‐4‐yl)pyridin‐4‐amine ( 1 ), was designed as a donor–acceptor system for incorporation into electronically active metal–organic frameworks (MOFs). The capacity for the ligand to undergo multiple sequential oxidation and reduction processes was examined using UV/Vis‐near‐infrared spectroelectrochemistry (UV/Vis‐NIR SEC) in combination with DFT calculations. The delocalized nature of the highest occupied molecular orbital (HOMO) was found to inhibit charge‐transfer interactions between the terminal triarylamine moieties upon oxidation, whereas radical species localized on the TzTz core were formed upon reduction. Conversion of 1 to diamagnetic 2+ and 4+ species resulted in marked changes in the emission spectra. Incorporation of this highly delocalized multi‐electron donor–acceptor ligand into a new two‐dimensional MOF, [Zn(NO₃)₂( 1 )] ( 2 ), resulted in an inhibition of the oxidation processes, but retention of the reduction capability of 1 . Changes in the electrochemistry of 1 upon integration into 2 are broadly consistent with the geometric and electronic constraints enforced by ligation.     

Super‐Resolution Imaging of the Golgi in Live Cells with a Bioorthogonal Ceramide Probe

We report a lipid‐based strategy to visualize Golgi structure and dynamics at super‐resolution in live cells. The method is based on two novel reagents: a trans‐cyclooctene‐containing ceramide lipid (Cer‐TCO) and a highly reactive, tetrazine‐tagged near‐IR dye (SiR‐Tz). These reagents assemble via an extremely rapid “tetrazine‐click” reaction into Cer‐SiR, a highly photostable “vital dye” that enables prolonged live‐cell imaging of the Golgi apparatus by 3D confocal and STED microscopy. Cer‐SiR is nontoxic at concentrations as high as 2 μM and does not perturb the mobility of Golgi‐resident enzymes or the traffic of cargo from the endoplasmic reticulum through the Golgi and to the plasma membrane.     

Gold‐Catalyzed Diastereoselective Cycloisomerization of Alkylidene‐Cyclopropane‐Bearing 1,6‐Diynes

An unprecedented gold‐catalyzed diastereoselective cycloisomerization of 1,6‐diynes bearing an alkylidene cyclopropane moiety has been developed. This methodology enables rapid access to a variety of 1,2‐trimethylenenorbornanes, which are important building blocks in the preparations of abiotic and sesquiterpene core structures.     

Metal‐Free Catalyst for the Chemoselective Methylation of Amines Using Carbon Dioxide as a Carbon Source

N‐methylation of amines is an important step in the synthesis of many pharmaceuticals and has been widely applied in the preparation of other key intermediates and chemicals. Therefore, the development of efficient methylation methods has attracted considerable attention. In this respect, carbon dioxide is an attractive C₁ building block because it is an abundant, renewable, and nontoxic carbon source. Consequently, we developed a highly chemoselective, metal‐free catalytic system that operates under ambient conditions for the N‐methylation of amines.     

Ab Initio H2O in Realistic Hydrophilic Confinement

A protocol for the ab initio construction of a realistic cylindrical pore in amorphous silica, serving as a geometric nanoscale confinement for liquids and solutions, is presented. Upon filling the pore with liquid water at different densities, the structure and dynamics of the liquid inside the confinement can be characterized. At high density, the pore introduces long‐range oscillations into the water density profile, which makes the water structure unlike that of the bulk across the entire pore. The tetrahedral structure of water is also affected up to the second solvation shell of the pore wall. Furthermore, the effects of the confinement on hydrogen bonding and diffusion, resulting in a weakening and distortion of the water structure at the pore walls and a slowdown in diffusion, are characterized.     

Cross-Link-Functionalized Nanoparticles for Rapid Excretion in Nanotheranostic Applications

Most NIR-IIb fluorophores are nanoparticle-based probes with long retention (≈1 month or longer) in the body. Here, we applied a novel cross-linked coating to functionalize core/shell lead sulfide/cadmium sulfide quantum dots (PbS/CdS QDs) emitting at ≈1600 nm. The coating was comprised of an amphiphilic polymer followed by three crosslinked amphiphilic polymeric layers (P³ coating), imparting high biocompatibility and >90 % excretion of QDs within 2 weeks of intravenous administration. The P³-QDs were conjugated to an engineered anti-CD8 diabody (Cys-diabody) for in vivo molecular imaging of CD8+ cytotoxic T lymphocytes (CTLs) in response to anti-PD-L1 therapy. Two-plex molecular imaging in combination with down-conversion Er nanoparticles (ErNPs) was performed for real-time in vivo monitoring of PD-L1 positive tumor cells and CTLs with cellular resolution by non-invasive NIR-IIb light sheet microscopy. Imaging of angiogenesis in the tumor microenvironment and of lymph nodes deep in the body with a signal-to-background ratio of up to ≈170 was also achieved using P³-QDs.     

Catalyst-Controlled Transannular Polyketide Cyclization Cascades: Selective Folding of Macrocyclic Polyketides

The biomimetic synthesis of aromatic polyketides from macrocyclic substrates by means of catalyst-controlled transannular cyclization cascades is described. The macrocyclic substrates, which feature increased stability and fewer conformational states, were thereby transformed into several distinct polyketide scaffolds. The catalyst-controlled transannular cyclizations selectively led to aromatic polyketides with a defined folding and oxygenation pattern, thus emulating β-keto-processing steps of polyketide biosynthesis.     

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.