Reaction-based machine learning representations for predicting the enantioselectivity of organocatalysts

Hundreds of catalytic methods are developed each year to meet the demand for high-purity chiral compounds. The computational design of enantioselective organocatalysts remains a significant challenge, as catalysts are typically discovered through experimental screening. Recent advances in combining quantum chemical computations and machine learning (ML) hold great potential to propel the next leap forward in asymmetric catalysis. Within the context of quantum chemical machine learning (QML, or atomistic ML), the ML representations used to encode the three-dimensional structure of molecules and evaluate their similarity cannot easily capture the subtle energy differences that govern enantioselectivity. Here, we present a general strategy for improving molecular representations within an atomistic machine learning model to predict the DFT-computed enantiomeric excess of asymmetric propargylation organocatalysts solely from the structure of catalytic cycle intermediates. Mean absolute errors as low as 0.25 kcal mol⁻¹ were achieved in predictions of the activation energy with respect to DFT computations. By virtue of its design, this strategy is generalisable to other ML models, to experimental data and to any catalytic asymmetric reaction, enabling the rapid screening of structurally diverse organocatalysts from available structural information.

A machine learning model for enantioselectivity prediction using reaction-based molecular representations.     

Azobioisosteres of Curcumin with Pronounced Activity against Amyloid Aggregation,Intracellular Oxidative Stress,and Neuroinflammation

Many (poly-)phenolic natural products, for example, curcumin and taxifolin, have been studied for their activity against specific hallmarks of neurodegeneration, such as amyloid-β 42 (Aβ42) aggregation and neuroinflammation. Due to their drawbacks, arising from poor pharmacokinetics, rapid metabolism, and even instability in aqueous medium, the biological activity of azobenzene compounds carrying a pharmacophoric catechol group, which have been designed as bioisoteres of curcumin has been examined. Molecular simulations reveal the ability of these compounds to form a hydrophobic cluster with Aβ42, which adopts different folds, affecting the propensity to populate fibril-like conformations. Furthermore, the curcumin bioisosteres exceeded the parent compound in activity against Aβ42 aggregation inhibition, glutamate-induced intracellular oxidative stress in HT22 cells, and neuroinflammation in microglial BV-2 cells. The most active compound prevented apoptosis of HT22 cells at a concentration of 2.5 μm (83 % cell survival), whereas curcumin only showed very low protection at 10 μm (21 % cell survival).     

Testosterone metabolism revisited: discovery of new metabolites

The metabolism of testosterone is revisited. Four previously unreported metabolites were detected in urine after hydrolysis with KOH using a liquid chromatography–tandem mass spectrometry method and precursor ion scan mode. The metabolites were characterized by a product ion scan obtained with accurate mass measurements. Androsta-4,6-dien-3,17-dione, androsta-1,4-dien-3,17-dione, 17-hydroxy-androsta-4,6-dien-3-one and 15-androsten-3,17-dione were proposed as feasible structures for these metabolites on the basis of the mass spectrometry data. The proposed structures were confirmed by analysis of synthetic reference compounds. Only 15-androsten-3,17-dione could not be confirmed, owing to the lack of a commercially available standard. That all four compounds are testosterone metabolites was confirmed by the qualitative analysis of several urine samples collected before and after administration of testosterone undecanoate. The metabolite androsta-1,4-dien-3,17-dione has a structure analogous to that of the exogenous anabolic steroid boldenone. Specific transitions for boldenone and its metabolite 17β-hydroxy-5β-androst-1-en-3-one were also monitored. Both compounds were also detected after KOH treatment, suggesting that this metabolic pathway is involved in the endogenous detection of boldenone previously reported by several authors.     

Determination of the dimerization constant of pinacyanol: role of the thermochromic effect

Pinacyanol (PIN), as other cyanine dyes, has demonstrated a unique ability to form associates such as dimers, and H- and J-aggregates. This association is strongly favoured in water, and even at low dye concentrations, dimers and superior order aggregates are present. As a consequence, the determination of the dimerization constant involves sometimes a significant error when these aggregates are neglected. As an increase in temperature shifts the equilibrium among the different species towards the lowest order aggregates, we have obtained the spectra of PIN at several temperatures. By extrapolating some spectral characteristics at high temperatures, a spectrum of the dimer without any contribution of other aggregates was obtained. From this spectrum and that of the monomer, the dimerization constant was calculated, as well as the Gibbs energy change associated to the reaction. The enthalpy and entropy changes of the dimerization were determined from the dependence of the dimerization constants on the temperature. From these results it can be inferred that the driving force of the dimerization is of enthalpic origin.     

Bandgap Modulation in Efficient n‐Thiophene Absorbers for Dye Solar Cell Sensitization

Five new sensitizers for dye sensitized solar cells have been designed consisting of conjugated thienylenevinylene units threaded with alkyl chains to improve solubility and cyanoacetic acid as anchoring group. The conjugation length was increased from 2 to 6 thienylenevinylene units, which resulted in a red‐shift of the optical absorption of the dyes from 550 to 750 nm, improving the spectral overlap with the solar spectrum. The photovoltaic performance of these dyes as sensitizers in mesoporous TiO₂ solar cells shows a clear correlation of increasing photocurrent with the extension of the conjugation up to an optimal length. Further extension of the conjugation increases the absorption but additional effects like self‐quenching or recombination processes reduce the photocurrent and photovoltages and consequently the overall efficiency of the DSC.     

Recovery stress and work output in hyperbranched poly(ethyleneimine)‐modified shape‐memory epoxy polymers

In this study a series of hyperbranched modified shape‐memory polymers were subjected to constrained shape recoveries in order to determine their potential use as thermomechanical actuators. Materials were synthesized from a diglycidyl ether of bisphenol A as base epoxy and a polyetheramine and a commercial hyperbranched poly(ethyleneimine) as crosslinker agents. Hyperbranched polymers within the structure of the shape‐memory epoxy polymers led to a more heterogeneous network that can substantially modify mechanical properties. Thermomechanical and mechanical properties were analyzed and discussed in terms of the content of hyperbranched polymer. Shape‐memory effect was analyzed under fully and partially constrained conditions. When shape recovery was carried out with fixed strain a recovery stress was obtained whereas when it was carried out with a constraining stress the material performs mechanical work. Tensile tests at Tg^E′ showed excellent values of stress and strain at break (up to 15 MPa and almost 60%, respectively). Constrained recovery performances revealed rapid recovery stress generation and unusually high recovery stresses (up to 7 MPa) and extremely high work densities (up to 750 kJ/m³). The network structure of shape‐memory polymers was found to be a key factor for actuator‐like applications. Results confirm that hyperbranched modified‐epoxy shape memory polymers are good candidates for actuator‐like shape‐memory applications. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1002–1013     

On the Binding of Congo Red to Amyloid Fibrils

Amyloids are characterized by their capacity to bind Congo red (CR), one of the most used amyloid‐specific dyes. The structural features of CR binding were unknown for years, mainly because of the lack of amyloid structures solved at high resolution. In the last few years, solid‐state NMR spectroscopy enabled the determination of the structural features of amyloids, such as the HET‐s prion forming domain (HET‐s PFD), which also has recently been used to determine the amyloid–CR interface at atomic resolution. Herein, we combine spectroscopic data with molecular docking, molecular dynamics, and excitonic quantum/molecular mechanics calculations to examine and rationalize CR binding to amyloids. In contrast to a previous assumption on the binding mode, our results suggest that CR binding to the HET‐s PFD involves a cooperative process entailing the formation of a complex with 1:1 stoichiometry. This provides a molecular basis to explain the bathochromic shift in the maximal absorbance wavelength when CR is bound to amyloids.