Freezing Capture of Polymorphic Aggregates of Bolaamphiphilic L‐Valine‐Based Molecular Hydrogelators

Nanostructured xerogels have been prepared by the freeze‐drying of hydrogels and aggregates formed by bolaamphiphilic L ‐valine derivatives after aging under different environmental conditions. A wide variety of shapes and sizes has been achieved by a simple methodology. These nanostructures have been studied by SEM and WAXD and a dramatic influence of structural flexibility on the kinetics of aggregation has been observed. Such flexibility and a modulation of the hydrophobic effect have shown a profound influence in the packing of these compounds and revealed a high degree of polymorphism.     

ChemStable: a web server for rule-embedded naïve Bayesian learning approach to predict compound stability

Predicting compound chemical stability is important because unstable compounds can lead to either false positive or to false negative conclusions in bioassays. Experimental data (COMDECOM) measured from DMSO/H₂O solutions stored at 50 °C for 105 days were used to predicted stability by applying rule-embedded naïve Bayesian learning, based upon atom center fragment (ACF) features. To build the naïve Bayesian classifier, we derived ACF features from 9,746 compounds in the COMDECOM dataset. By recursively applying naïve Bayesian learning from the data set, each ACF is assigned with an expected stable probability (p _s ) and an unstable probability (p _uns ). 13,340 ACFs, together with their p _s and p _uns data, were stored in a knowledge base for use by the Bayesian classifier. For a given compound, its ACFs were derived from its structure connection table with the same protocol used to drive ACFs from the training data. Then, the Bayesian classifier assigned p _s and p _uns values to the compound ACFs by a structural pattern recognition algorithm, which was implemented in-house. Compound instability is calculated, with Bayes’ theorem, based upon the p _s and p _uns values of the compound ACFs. We were able to achieve performance with an AUC value of 84 % and a tenfold cross validation accuracy of 76.5 %. To reduce false negatives, a rule-based approach has been embedded in the classifier. The rule-based module allows the program to improve its predictivity by expanding its compound instability knowledge base, thus further reducing the possibility of false negatives. To our knowledge, this is the first in silico prediction service for the prediction of the stabilities of organic compounds.     

X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X-ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand-FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X-ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno-oncology.     

Controlled Generation of 9-Boratriptycene by Lewis Adduct Dissociation: Accessing a Non-Planar Triarylborane

A highly bent triarylborane, 9-boratriptycene, was generated in solution by selective protodeboronation of the corresponding tetra-aryl boron ate complex with the strong Brønsted acid HNTf₂. The iptycene core confers enhanced Lewis acidity to 9-boratriptycene, making it unique in terms of structure and reactivity. We studied the stereoelectronic properties of 9-boratriptycene by quantifying its association with small N- and O-centered Lewis bases, as well as with sterically hindered phosphines. The resultant Lewis adducts exhibited unique structural, spectroscopic, and photophysical properties. Beyond the high pyramidalization of the 9-boratriptycene scaffold and its low reorganization energy upon Lewis base coordination, quantum chemical calculations revealed that the absence of π donation from the triptycene aryl rings to the boron vacant p_z orbital is one of the main reasons for its high Lewis acidity.     

Covalent Adaptable Networks with Tunable Exchange Rates Based on Reversible Thiol–yne Cross‐Linking

The design of covalent adaptable networks (CANs) relies on the ability to trigger the rearrangement of bonds within a polymer network. Simple activated alkynes are now used as versatile reversible cross‐linkers for thiols. The click‐like thiol–yne cross‐linking reaction readily enables network synthesis from polythiols through a double Michael addition with a reversible and tunable second addition step. The resulting thioacetal cross‐linking moieties are robust but dynamic linkages. A series of different activated alkynes have been synthesized and systematically probed for their ability to produce dynamic thioacetal linkages, both in kinetic studies of small molecule models, as well as in stress relaxation and creep measurements on thiol–yne‐based CANs. The results are further rationalized by DFT calculations, showing that the bond exchange rates can be significantly influenced by the choice of the activated alkyne cross‐linker.     

Dendrobeaniamine A,a new alkaloid from the Arctic marine bryozoan Dendrobeania murrayana

Abstract

The new guanidine alkaloid Dendrobeaniamine A (1) was isolated from the organic extract of the Arctic marine bryozoan Dendrobeania murrayana. The chemical structure of 1 was elucidated by spectroscopic experiments, including 1D and 2D NMR and HRESIMS analysis. Compound 1 is a lipoamino acid, consisting of a C₁₂ fatty acid anchored to the amino acid arginine. The bioactivity of 1 was evaluated using cellular and biochemical assays, but the compound did not show cytotoxic, antimicrobial, anti-inflammatory or antioxidant activities     

Formation and Structure of Fluorescent Silver Nanoclusters at Interfacial Binding Sites Facilitating Oligomerization of DNA Hairpins

Fluorescent, DNA‐stabilized silver nanoclusters (DNA‐AgNCs) are applied in a range of applications within nanoscience and nanotechnology. However, their diverse optical properties, mechanism of formation, and aspects of their composition remain unexplored, making the rational design of nanocluster probes challenging. Herein, a synthetic procedure is described for obtaining a high yield of emissive DNA‐AgNCs with a C‐loop hairpin DNA sequence, with subsequent purification by size‐exclusion chromatography (SEC). Through a combination of optical spectroscopy, gel electrophoresis, inductively coupled plasma mass spectrometry (ICP‐MS), and small‐angle X‐ray scattering (SAXS) in conjunction with the systematic study of various DNA sequences, the low‐resolution structure and mechanism of the formation of AgNCs were investigated. Data indicate that fluorescent DNA‐AgNCs self‐assemble by a head‐to‐head binding of two DNA hairpins, bridged by a silver nanocluster, resulting in the modelling of a dimeric structure harboring an Ag₁₂ cluster.     

基于碳水化合物的阳离子聚合物载体在基因释放中的应用

在基因治疗中,基因释放载体是不可缺少的重要组成部分.近几年来聚合物基因释放载体的研究主要旨在开发低毒或无毒的阳离子聚合物用于安全有效的基因释放.作为一类天然化合物,基于碳水化合物的阳离子聚合物载体由于其良好的生物相容性和低毒性被广泛地研究并应用于基因释放.本文阐述了聚合物基因释放的机理,并对近几年来一些典型的含碳水化合物的阳离子聚合物基因释放载体作一综述.     

Surface Functionalization of Magnetite Nanoparticles with Multipotent Antioxidant as Potential Magnetic Nanoantioxidants and Antimicrobial Agents

Functionalized magnetite nanoparticles (Fe₃O₄) were prepared using the coprecipitation method followed by functionalization with a multipotent antioxidant (MPAO). The MPAO was synthesized and analyzed using FTIR and NMR techniques. In this study, the functionalized nanoparticles (IONP@AO) were produced and evaluated using the FTIR, XRD, Raman, HRTEM, FESEM, VSM, and EDX techniques. The average determined particle size of IONP@AO was 10 nanometers. In addition, it demonstrated superparamagnetic properties. The magnitude of saturation magnetization value attained was 45 emu g⁻¹. Virtual screenings of the MPAO’s potential bioactivities and safety profile were performed using PASS analysis and ADMET studies before the synthesis step. For the DPPH test, IONP@AO was found to have a four-fold greater ability to scavenge free radicals than unfunctional IONP. The antimicrobial properties of IONP@AO were also demonstrated against a variety of bacteria and fungi. The interaction of developed nanoantioxiants with biomolecules makes it a broad-spectrum candidate in biomedicine and nanomedicine.     

Radial flow velocity profiles of a yield stress fluid between smooth parallel disks

In rock grouting, idealized 2D-radial laminar flow of yield stress fluids (YSF) is a fundamental flow configuration that is used for cement grout spread estimation. A limited amount of works have presented analytical and numerical solutions on the radial velocity profiles between parallel disks. However, to the best of our knowledge, there has been no experimental work that has presented measured velocity profiles for this geometry. In this paper, we present velocity profiles of Carbopol (a simple YSF), measured by pulsed ultrasound velocimetry within a radial flow model. We describe the design of the physical model and then present the measured velocity profiles while highlighting the plug-flow region and slip effects observed for three different apertures and volumetric flow rates. Although the measured velocity profiles exhibited wall slip, there was a reasonably good agreement with the analytical solution. We then discuss the major implications of our work on radial flow.