Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem

Revealing the Phase Separation Behavior of Thermodynamically Immiscible Elements in a Nanoparticle.

Phase-separation is commonly observed in multimetallic nanomaterials, yet it is not well understood how immiscible elements distribute in a thermodynamically stable nanoparticle. Herein, we studied the phase-separation of Au and Rh in nanoparticles using electron microscopy and tomography techniques. The nanoparticles were thermally annealed to form thermodynamically stable structures. HAADF-STEM and EDS characterizations reveal that Au and Rh segregate into two domains while their miscibility is increased. Using aberration-corrected HAADF-STEM and atomic electron tomography, we show that the increased solubility of Au in Rh is achieved by forming Au clusters and single atoms inside the Rh domains and on the Rh surface. Furthermore, based on the three-dimensional reconstruction of a AuRh nanoparticle, we can visualize the uneven interface that is embedded in the nanoparticle. The results advance our understanding on the nanoscale thermodynamic behavior of metal mixtures, which is crucial for the optimization of multimetallic nanostructures for many applications

Improved photocatalytic Bi₂WO₆/BiOCl heterojunctions:one-step synthesis via an ionic-liquid assisted ultrasonic method and first-principles calculations

Abstract Bi₂WO₆/BiOCl heterojunctions with high photocatalytic activity and photocurrent property were synthesized via an ionic-liquid assisted ultrasonic irradiation at room temperature. The ionic liquid 1-butyl-3-methylimidazolium chloride ([BMIM]Cl) was used as the Cl source. Modifications of heterojunction structures and properties were realized just by changing the amount of [BMIM]Cl. Photocatalytic activities of Bi₂WO₆/BiOCl heterojunctions enable fast degradations of 2,4-dinitrophenol solution (DNP), rhodamine B (RhB) and quinoline blue (QB) under visible light and sunlight irradiation. Through first-principles calculations, the Bi-O bonding was found as junction structures at the interface, leading to band intercalations between the two parts besides the interface. Efficient charge (hole) transfers to two sides of the tungstate and chloride were enabled through interface during photocatalytic processes, resulting in longer electron-hole separations, and enhanced catalytic activities under sunlight radiation. The mechanism is crosschecked with transient photocurrent results where the BiOCl-Bi₂WO₆ heterojunction possess higher photocurrent than pure Bi₂WO₆ or BiOCl, ascribed to inhibition of electron-hole recombination in the photo processes

Energy Funneling in a Noninteger Two-Dimensional Perovskite

Energy funneling is a phenomenon that has been exploited in optoelectronic devices based on low-dimensional materials to improve their performance. Here, we introduce a new class of two-dimensional semiconductor, characterized by multiple regions of varying thickness in a single confined nanostructure with homogeneous composition. This "noninteger 2D semiconductor" was prepared via the structural transformation of two-octahedron-layer-thick (n = 2) 2D cesium lead bromide perovskite nanosheets; it consisted of a central n = 2 region surrounded by edge-lying n = 3 regions, as imaged by electron microscopy. Thicker noninteger 2D CsPbBr3 nanostructures were obtained as well. These noninteger 2D perovskites formed a laterally coupled quantum well band alignment with virtually no strain at the interface and no dielectric barrier, across which unprecedented intramaterial funneling of the photoexcitation energy was observed from the thin to the thick regions using time-resolved absorption and photoluminescence spectroscopy

Direct Observation of Transient Structural Dynamics of Atomically Thin Halide Perovskite Nanowires

Halide perovskite is a unique dynamical system, whose structural and chemical processes happening across different timescales have significant impact on its physical properties and device-level performance. However, due to its intrinsic instability, real-time investigation of the structure dynamics of halide perovskite is challenging, which hinders the systematic understanding of the chemical processes in the synthesis, phase transition, and degradation of halide perovskite. Here, we show that atomically thin carbon materials can stabilize ultrathin halide perovskite nanostructures against otherwise detrimental conditions. Moreover, the protective carbon shells enable atomic-level visualization of the vibrational, rotational, and translational movement of halide perovskite unit cells. Albeit atomically thin, protected halide perovskite nanostructures can maintain their structural integrity up to an electron dose rate of 10,000 e-/Å2·s while exhibiting unusual dynamical behaviors pertaining to the lattice anharmonicity and nanoscale confinement. Our work demonstrates an effective method to protect beam-sensitive materials during in situ observation, unlocking new solutions to study new modes of structure dynamics of nanomaterials

A facile synthesis of heterojunctional BiVO₄/Bi₅O₇I with enhanced photocatalytic activity for organic dyes degradation

Abstract Photocatalysis technology has risen to effectively degrade the hardly-degraded organic pollutants in recent years and the photocatalysts play an important role in striding the obstacles of the visible light response. Herein, a high-efficiency BiVO₄/Bi₅O₇I heterojunctional photocatalysts have been purposefully designed by controlling the reactant ratios and ultrasonic time of reaction at room temperature. Photocatalytic experimentals confirm that the prepared optimal BiVO₄/Bi₅O₇I composites displayed enhanced photocatalytic ability to degrade rhodamine B and quinoline blue under visible light irradiation. Furthermore, the photocatalysts exhibits high photostability and reusability proved by four consecutive cycling experiments. A possible mechanism of p–n heterojunctional BiVO₄/Bi₅O₇I composites enhanced the photocatalytic performance was discussed in detail on the basis of the reactive species trapping experiments in photocatalytic degradation process