Research articles

Automated free energy calculations for the prediction of binding free energies of ligands to a protein target are gaining importance for drug discovery, but building reliable initial binding poses for the ligands is challenging. Here, the authors introduce an open-source workflow for building user-defined congeneric series of ligands in protein binding pockets for input to free energy calculations.

Studying the excitation energy transfer from carotenoids to bacteriochlorophyll a in purple photosynthetic bacteria could provide insights on how to optimize photosynthetic light-harvesting. Here, the authors study a carotenoid reconstituted core light-harvesting 1 complex from Rhodospirillum rubrum and find that the involvement of the intramolecular charge-transfer excited state of β-apo-8′-carotenal plays a key role in achieving an excitation energy transfer efficiency of ~77%.

Metal oxide nanoparticles functionalized by organic molecules are important building blocks for nanocomposites. Here, the authors study the adsorption of oleic acid on magnetite (001) and (111) surfaces experimentally by SXRD, LEED, FT-IRRAS and XRR, and employ a molecular dynamics force field specifically developed for magnetite/organic interfaces to determine molecular adsorption geometries, coverages, layer thicknesses and adsorption-induced structural changes in the substrate.

Silver-catalyzed hydroamidation of siloxy-alkynes is a successful approach for the hydroamidation of internal alkynes, however the mechanism of this reaction is poorly understood. Here, the authors use density functional theory calculations to reveal that the reaction takes place through a silver activated silylium ion migration mediated hydroamidation pathway.

Understanding the relative strengths of metal–ligand and metal–metal interactions in ligated nanoclusters is key to tailoring their properties. Here, collision-induced dissociation of two series of atomically precise metal sulfide nanoclusters provides insight into the modulation of the core–ligand interactions of the atomically precise metal chalcogenide clusters.

Deep generative neural networks are increasingly exploited for drug discovery, but often the majority of generated molecules are predicted to be inactive. Here, an optimized protocol for generative models with reinforcement learning is derived and applied to design potent epidermal growth factor inhibitors.

Alanine substitution in peptides is crucial for studying peptide-based inhibitors of protein–protein interactions, but limited information is obtained from single alanine substitution. Here, the authors develop a label-free combinatorial alanine affinity selection platform to establish multi-alanine mutational tolerance and provide structure-activity relationships.

The electronic structures and open-shell diradical character of organic diradicaloids endow them with potentially useful optical, electronic and magnetic properties. Here, an open-shell nitrogen-centered diradicaloid is reported and shown to readily react with Lewis and Brønsted acids to form acid-base adducts, allowing for tuning of ground-state electronic structure, diradical character and spin density distribution.

Electrocatalytic oxygen evolution is a key reaction for water splitting, but the detailed atomic structures of single-crystal electrodes under cycling conditions are still not fully understood. Here, the authors study the oxygen evolution activity on Pt(111) during potential cycling and find that the current density reaches a maximum in the third cycle and is nine times higher than that in the initial cycle, owing to a roughened Pt(111) surface and formation of islands and atomic vacancies in the second subsurface Pt layer.

Coupling the photo-oxidation of biomass-derived substrates with water splitting in a photoelectrochemical cell enables efficient hydrogen generation at the cathode. Here, a photoelectrochemical device employing a nanostructured WO₃ photoanode displays photocurrents of 6.5 mA cm⁻² through oxidation of glucose, in turn producing valuable products in the form of gluconic and glucaric acids, erythrose and arabinose.

Direct conversion of methane to methanol has great industrial relevance, but required high reaction temperatures can lead to overoxidation of methane to carbon dioxide. Here, methanol is synthesized by one-step reaction of methane and water over a TiO₂ catalyst in a non-thermal plasma at room temperature and atmospheric pressure, which allows to isolate carbon dioxide-free methanol.

The chemical stability of alkali halides has caused them to be exploited as inert media in high-pressure, high-temperature experiments. Here, NaCl and KCl are unexpectedly found to react with yttrium, dysprosium and iron oxide in a laser-heated diamond anvil cell, producing Y₂Cl, DyCl, Y₂ClC and Dy₂ClC at ~40 GPa and 2000 K and FeCl₂ at ~160 GPa and 2100 K.

Imine reductases can catalyze reductive amination reactions to produce chiral amines, however, transformation of bulky amines has been challenging. Here, by using an increasing-molecule-volume-screening method, the authors identify a group of imine reductases that can accept bulky amines and achieve an efficient gram-scale synthesis of an API sensipar analogue.

Structural defects in metal–organic frameworks can be exploited to tune material properties. Here, a combined theoretical and experimental study demonstrates that the introduction of defects to UiO-66 alters its nature from hydrophobic to hydrophilic, affecting the adsorption mechanism of polar and non-polar molecules.

Polymeric solid foams have several beneficial properties such as their light weight, thermal insulation or shock absorbance, but it is still challenging to efficiently control the foam architecture. Here, the authors optimize the frontal polymerization of dicyclopentadiene with allyl-functionalized cellulose nanocrystals to rapidly achieve solid foams with modified structures and enhanced oxidation resistance.

Boron-containing materials have experimentally and theoretically been shown to be promising materials for CO₂ capture and conversion. Here, hydrogen-deficient 2D hydrogen boride sheets are shown to physisorb CO₂ and promote conversion to methane and ethane.

Trimethylamine N-oxide (TMAO) protects organisms from the damaging effects of deep-sea high pressure, but it is not well understood how pressure and TMAO in combination perturb the water structure. Here, the authors use neutron scattering coupled with computational modelling of water at 25 bar and 4 kbar in the presence and absence of TMAO to propose an “osmolyte protection ratio” at which pressure and TMAO-induced energy changes effectively cancel out, which translates across scales to the organism level.

The main protease (M^pro) of SARS-CoV-2 is an important target for COVID-19 therapy. Here, a pair of genetically encoded BRET-based sensors for detecting M^pro activity are generated by sandwiching N-terminal autocleavage sites in between the mNeonGreen and NanoLuc proteins.

Sustainable aviation fuels offer the opportunity to both reduce CO₂ emissions and produce fuels with superior properties to conventional petroleum-based fuels. Here, the bio-based monoterpene linalool is converted into an aviation fuel mixture primarily composed of p-menthane and 2,6-dimethyloctane at moderate temperatures and pressures using a combination of Amberlyst-15 and Pd/C catalysts. The resulting fuel is demonstrated to have a higher gravimetric heat of combustion, and a lower viscosity compared to petroleum derived Jet-A.

Iron is the most abundant redox active transition metal in mineral dust, but its role in nitrogen-containing organic carbon formation remains largely unexplored. Here, the authors show that Fe(III) catalyzes the dark oxidative oligomerization of o- and p-aminophenols under simulated aerosol and cloud conditions.