Structure-Activity Relationship of Oxacyclo- and Triazolo-Containing Respiratory Syncytial Virus Polymerase Inhibitors.

Despite the availability of medicines preventing respiratory syncytial virus (RSV) infection, post-exposure treatment options are needed for addressing patient's needs. RSV non-nucleoside polymerase inhibitors (NNI) have emerged as a promising asset for which our group previously disclosed JNJ-8003 with potent in vitro antiviral activity and pronounced in vivo efficacy. In this work, a structural-guided design to modify the linker vector of JNJ-8003 resulted in the identification of 2-oxacyclo pyridine-containing derivatives whose various ring closing strategies are described. In addition, bioisosteric replacement of an amide bond with triazole retained potency, and cryo-electron microscopy (cryo-EM) confirmed binding in the capping domain. Subsequent NMR conformational analysis suggested a correlation between the potency and conformations. Our efforts have fulfilled the aim of identifying linker modifications with maintained biological activity while enriching structural diversity and allowing modulations of other parameters.

Through thickness anisotropy in all inorganic perovskite thin films via two-step synthesis: implications for voltaic devices.

Cesium-lead-bromide (CsPbBr3) has shown promise in thin film photovoltaics due to its desirable energy band gap, charge mobility and chemical and thermal stability. The low solubility of its single crystal in organic solvents has driven development of the two-step spin-coating technique. In this work, precursor solutions of different PbBr2 and CsBr concentrations were spin-coated and investigated via Photoelectron Spectroscopy. The properties of the CsxPbyBrz film in cross-section demonstrate this method leads to varying stoichiometries, work functions and band gaps through the thickness. This anisotropy of the perovskite thickness has ramifications for design of photovoltaic devices.

Spectroscopic analysis of nanosized Zn(Ag, Ni)O systems and observation of superparamagnetism at low temperature.

To understand the impact of binary doping in ZnO, nanosized Zn(Ag, Ni)O systems were synthesized by the sol-gel method. The amount of Ag was fixed at 2 at%, and that of Ni was varied from 1 to 15 at%. Ni incorporation equal to or beyond 3 at% gave rise to the development of the NiO phase. The presence of Ag and Ni did not have much influence on the lattice constants of ZnO. However, a larger addition of Ni impacted the unit cell of NiO, as indicated by the reduction of the lattice constant of NiO. The increase in NiO and Ag contents in ZnO reduced the second and third harmonic intensities under non-linear investigations. X-ray photoelectron spectroscopy analysis indicated that initial Ni addition varied randomly along with Ag, and it stabilized itself at higher concentration. Field emission scanning electron microscopy revealed that interlinked particles and chains with tamarind shapes were formed, closely matching the rod-like structures under high resolution. Ag and Ni addition altered the structures slightly and randomly till 5 at% Ni; thereafter they deviated from the particle shape to flat disc-shapes. Interestingly, the magnetic response of the sample was determined by the NiO phase, and the effect of Ni and Ag substitution in the ZnO host matrix was almost irrelevant at low temperatures toward magnetic contribution. Weak ferromagnetism at low temperatures (≤50 K) with superparamagnetic-like behavior (cusp in ZFC magnetization) was observed in all the samples. This could be attributed to the finite nano-size effect and uncompensated spins at the surface of the particle.

Probing the CRL4DCAF12 interactions with MAGEA3 and CCT5 di-Glu C-terminal degrons.

Damaged DNA-binding protein-1 (DDB1)- and CUL4-associated factor 12 (DCAF12) serves as the substrate recognition component within the Cullin4-RING E3 ligase (CRL4) complex, capable of identifying C-terminal double-glutamic acid degrons to promote the degradation of specific substrates through the ubiquitin proteasome system. Melanoma-associated antigen 3 (MAGEA3) and T-complex protein 1 subunit epsilon (CCT5) proteins have been identified as cellular targets of DCAF12. To further characterize the interactions between DCAF12 and both MAGEA3 and CCT5, we developed a suite of biophysical and proximity-based cellular NanoBRET assays showing that the C-terminal degron peptides of both MAGEA3 and CCT5 form nanomolar affinity interactions with DCAF12 in vitro and in cells. Furthermore, we report here the 3.17 Šcryo-EM structure of DDB1-DCAF12-MAGEA3 complex revealing the key DCAF12 residues responsible for C-terminal degron recognition and binding. Our study provides new insights and tools to enable the discovery of small molecule handles targeting the WD40-repeat domain of DCAF12 for future proteolysis targeting chimera design and development.

Structural basis for the oligomerization-facilitated NLRP3 activation.

The NACHT-, leucine-rich-repeat-, and pyrin domain-containing protein 3 (NLRP3) is a critical intracellular inflammasome sensor and an important clinical target against inflammation-driven human diseases. Recent studies have elucidated its transition from a closed cage to an activated disk-like inflammasome, but the intermediate activation mechanism remains elusive. Here we report the cryo-electron microscopy structure of NLRP3, which forms an open octamer and undergoes a ~ 90° hinge rotation at the NACHT domain. Mutations on open octamer's interfaces reduce IL-1ß signaling, highlighting its essential role in NLRP3 activation/inflammasome assembly. The centrosomal NIMA-related kinase 7 (NEK7) disrupts large NLRP3 oligomers and forms NEK7/NLRP3 monomers/dimers which is a critical step preceding the assembly of the disk-like inflammasome. These data demonstrate an oligomeric cooperative activation of NLRP3 and provide insight into its inflammasome assembly mechanism.

Reduction and Diffusion of Cr-Oxide Layers into P25, BaLa4Ti4O15, and Al:SrTiO3 Particles upon High-Temperature Annealing.

Chromium oxide (Cr2O3) is a beneficial metal oxide used to prevent the backward reaction in photocatalytic water splitting. The present work investigates the stability, oxidation state, and the bulk and surface electronic structure of Cr-oxide photodeposited onto P25, BaLa4Ti4O15, and Al:SrTiO3 particles as a function of the annealing process. The oxidation state of the Cr-oxide layer as deposited is found to be Cr2O3 on the surface of P25 and Al:SrTiO3 particles and Cr(OH)3 on BaLa4Ti4O15. After annealing at 600 °C, for P25 (a mixture of rutile and anatase TiO2), the Cr2O3 layer diffuses into the anatase phase but remains at the surface of the rutile phase. For BaLa4Ti4O15, Cr(OH)3 converts to Cr2O3 upon annealing and diffuses slightly into the particles. However, for Al:SrTiO3, the Cr2O3 remains stable at the surface of the particles. The diffusion here is due to the strong metal-support interaction effect. In addition, some of the Cr2O3 on the P25, BaLa4Ti4O15, and Al:SrTiO3 particles is reduced to metallic Cr after annealing. The effect of Cr2O3 formation and diffusion into the bulk on the surface and bulk band gaps is investigated with electronic spectroscopy, electron diffraction, DRS, and high-resolution imaging. The implications of the stability and diffusion of Cr2O3 for photocatalytic water splitting are discussed.

Effect of TiO2 Film Thickness on the Stability of Au9 Clusters with a CrOx Layer.

Radio frequency (RF) magnetron sputtering allows the fabrication of TiO2 films with high purity, reliable control of film thickness, and uniform morphology. In the present study, the change in surface roughness upon heating two different thicknesses of RF sputter-deposited TiO2 films was investigated. As a measure of the process of the change in surface morphology, chemically -synthesised phosphine-protected Au9 clusters covered by a photodeposited CrOx layer were used as a probe. Subsequent to the deposition of the Au9 clusters and the CrOx layer, samples were heated to 200 ℃ to remove the triphenylphosphine ligands from the Au9 cluster. After heating, the thick TiO2 film was found to be mobile, in contrast to the thin TiO2 film. The influence of the mobility of the TiO2 films on the Au9 clusters was investigated with X-ray photoelectron spectroscopy. It was found that the high mobility of the thick TiO2 film after heating leads to a significant agglomeration of the Au9 clusters, even when protected by the CrOx layer. The thin TiO2 film has a much lower mobility when being heated, resulting in only minor agglomeration of the Au9 clusters covered with the CrOx layer.

Cr2O3 layer inhibits agglomeration of phosphine-protected Au9 clusters on TiO2 films.

The properties of semiconductor surfaces can be modified by the deposition of metal clusters consisting of a few atoms. The properties of metal clusters and of cluster-modified surfaces depend on the number of atoms forming the clusters. Deposition of clusters with a monodisperse size distribution thus allows tailoring of the surface properties for technical applications. However, it is a challenge to retain the size of the clusters after their deposition due to the tendency of the clusters to agglomerate. The agglomeration can be inhibited by covering the metal cluster modified surface with a thin metal oxide overlayer. In the present work, phosphine-protected Au clusters, Au9(PPh3)8(NO3)3, were deposited onto RF-sputter deposited TiO2 films and subsequently covered with a Cr2O3 film only a few monolayers thick. The samples were then heated to 200 °C to remove the phosphine ligands, which is a lower temperature than that required to remove thiolate ligands from Au clusters. It was found that the Cr2O3 covering layer inhibited cluster agglomeration at an Au cluster coverage of 0.6% of a monolayer. When no protecting Cr2O3 layer was present, the clusters were found to agglomerate to a large degree on the TiO2 surface.

Influence of TiO2 surface defects on the adsorption of N719 dye molecules.

Surface defects influence the dye adsorption on TiO2 used as a substrate in dye-sensitized solar cells (DSSCs). In this study, we have used different Ar+ sputtering doses to create a controlled density of defects on a TiO2 surface exposed to different pre-heating temperatures in order to analyse the influence of defects on the N719 dye adsorption. TiO2 was pre-treated using two different treatments. The first treatment involved heating to 200 °C with subsequent sputtering at different doses. The second treatment included heating only, but at four different temperatures starting at 200 °C. After the pre-treatments, the TiO2 samples were immersed into an N719 dye solution for 24 hours at room temperature to dye the TiO2 substrates. The amount of Ti3+ surface defects introduced by the different pre-treatments and their influence on dye adsorption onto the TiO2 surface were examined by X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS) and metastable induced electron spectroscopy (MIES). Neutral impact collision ion scattering spectroscopy (NICISS) was used to determine the coverage of the TiO2 surface by adsorbed dye molecules. It was found that Ti3+ surface defects were formed by Ar+ sputtering but not by pre-treatment through heating alone. MIES analysis of the outer-most layer and density of states calculations show that the thiocyanate ligand of the N719 dye becomes directed away from the TiO2 surface. Both XPS and NICISS results indicate that the amount of adsorbed N719 dye decreases with increasing density of Ti3+ surface defects. Thus, the generation of surface defects reduces the ability of the TiO2 surface to adsorb the dye molecules. Heating alone as pre-treatment of the TiO2 substrates instead increases the dye adsorption, without causing detectable defects on the TiO2 surface.

Carbonisation of a polymer made from sulfur and canola oil.

A polymer made from equal masses of sulfur and canola oil was carbonised at 600 °C for 30 minutes. The resulting material exhibited improved uptake of mercury from water compared to the polymer. The carbonisation could also be done after using the polymer to clean up oil spills, which suprisingly improved mercury uptake to levels rivaling commercial carbons.

Structural basis for aggregate dissolution and refolding by the Mycobacterium tuberculosis ClpB-DnaK bi-chaperone system.

The M. tuberculosis (Mtb) ClpB is a protein disaggregase that helps to rejuvenate the bacterial cell. DnaK is a protein foldase that can function alone, but it can also bind to the ClpB hexamer to physically couple protein disaggregation with protein refolding, although the molecular mechanism is not well understood. Here, we report the cryo-EM analysis of the Mtb ClpB-DnaK bi-chaperone in the presence of ATPγS and a protein substrate. We observe three ClpB conformations in the presence of DnaK, identify a conserved TGIP loop linking the oligonucleotide/oligosaccharide-binding domain and the nucleotide-binding domain that is important for ClpB function, derive the interface between the regulatory middle domain of the ClpB and the DnaK nucleotide-binding domain, and find that DnaK binding stabilizes, but does not bend or tilt, the ClpB middle domain. We propose a model for the synergistic actions of aggregate dissolution and refolding by the Mtb ClpB-DnaK bi-chaperone system.

The mycobacterial proteasomal ATPase Mpa forms a gapped ring to engage the 20S proteasome.

Although many bacterial species do not possess proteasome systems, the actinobacteria, including the human pathogen Mycobacterium tuberculosis, use proteasome systems for targeted protein removal. Previous structural analyses of the mycobacterial proteasome ATPase Mpa revealed a general structural conservation with the archaeal proteasome-activating nucleotidase and eukaryotic proteasomal Rpt1-6 ATPases, such as the N-terminal coiled-coil domain, oligosaccharide-/oligonucleotide-binding domain, and ATPase domain. However, Mpa has a unique ß-grasp domain that in the ADP-bound crystal structure appears to interfere with the docking to the 20S proteasome core particle (CP). Thus, it is unclear how Mpa binds to proteasome CPs. In this report, we show by cryo-EM that the Mpa hexamer in the presence of a degradation substrate and ATP forms a gapped ring, with two of its six ATPase domains being highly flexible. We found that the linkers between the oligonucleotide-binding and ATPase domains undergo conformational changes that are important for function, revealing a previously unappreciated role of the linker region in ATP hydrolysis-driven protein unfolding. We propose that this gapped ring configuration is an intermediate state that helps rearrange its ß-grasp domains and activating C termini to facilitate engagement with proteasome CPs. This work provides new insights into the crucial process of how an ATPase interacts with a bacterial proteasome protease.

Au101-rGO nanocomposite: immobilization of phosphine-protected gold nanoclusters on reduced graphene oxide without aggregation.

Graphene supported transition metal clusters are of great interest for potential applications, such as catalysis, due to their unique properties. In this work, a simple approach to deposit Au101(PPh3)21Cl5 (Au101NC) on reduced graphene oxide (rGO) via an ex situ method is presented. Reduction of graphene oxide at native pH (pH ≈ 2) to rGO was performed under aqueous hydrothermal conditions. Decoration of rGO sheets with controlled content of 5 wt% Au was accomplished using only pre-synthesised Au101NC and rGO as precursors and methanol as solvent. High resolution scanning transmission electron microscopy indicated that the cluster size did not change upon deposition with an average diameter of 1.4 ± 0.4 nm. It was determined that the rGO reduction method was crucial to avoid agglomeration, with rGO reduced at pH ≈ 11 resulting in agglomeration. X-ray photoelectron spectroscopy was used to confirm the deposition of Au101NCs and show the presence of triphenyl phosphine ligands, which together with attenuated total reflectance Fourier transform infrared spectroscopy, advocates that the deposition of Au101NCs onto the surface of rGO was facilitated via non-covalent interactions with the phenyl groups of the ligands. Inductively coupled plasma mass spectrometry and thermogravimetric analysis were used to determine the gold loading and both agree with a gold loading of ca. 4.8-5 wt%. The presented simple and mild strategy demonstrates that good compatibility between size-specific phosphine protected gold clusters and rGO can prevent aggregation of the metal clusters. This work contributes towards producing an agglomeration-free synthesis of size-specific ligated gold clusters on rGO that could have wide range of applications.

In Situ Formation of Mixed-Dimensional Surface Passivation Layers in Perovskite Solar Cells with Dual-Isomer Alkylammonium Cations.

Dimensional engineering of perovskite solar cells has attracted significant research attention recently because of the potential to improve both device performance and stability. Here, a novel 2D passivation scheme for 3D perovskite solar cells is demonstrated using a mixed cation composition of 2D perovskite based on two different isomers of butylammonium iodide. The dual-cation 2D perovskite outperforms its single cation 2D counterparts in surface passivation quality, resulting in devices with an impressive open-circuit voltage of 1.21 V for a perovskite composition with an optical bandgap of ≈1.6 eV, and a champion efficiency of 23.27%. Using a combination of surface elemental analysis and valence electron spectra decomposition, it is shown that an in situ interaction between the 2D perovskite precursor and the 3D active layer results in surface intermixing of 3D and 2D perovskite phases, providing an effective combination of defect passivation and enhanced charge transfer, despite the semi-insulating nature of the 2D perovskite phase. The demonstration of the synergistic interaction of multiple organic spacer cations in a 2D passivation layer offers new opportunities for further enhancement of device performance with mixed dimensional perovskite solar cells.

Highly Stable Indacenodithieno[3,2-b]thiophene-Based Donor-Acceptor Copolymers for Hybrid Electrochromic and Energy Storage Applications.

Stable doping of indacenodithieno[3,2-b]thiophene (IDTT) structures enables easy color tuning and significant improvement in the charge storage capacity of electrochromic polymers, making use of their full potential as electrochromic supercapacitors and in other emerging hybrid applications. Here, the IDTT structure is copolymerized with four different donor-acceptor-donor (DAD) units, with subtle changes in their electron-donating and electron-withdrawing characters, so as to obtain four different donor-acceptor copolymers. The polymers attain important form factor requirements for electrochromic supercapacitors: desired switching between achromatic black and transparent states (L*a*b* 45.9, -3.1, -4.2/86.7, -2.2, and -2.7 for PIDTT-TBT), high optical contrast (72% for PIDTT-TBzT), and excellent electrochemical redox stability (Ired/Iox ca. 1.0 for PIDTT-EBE). Poly[indacenodithieno[3,2-b]thiophene-2,8-diyl-alt-4,7-bis(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-2-(2-hexyldecyl)-2H-benzo[d][1,2,3]triazole-7,7'-diyl] (PIDTT-EBzE) stands out as delivering simultaneously a high contrast (69%) and doping level (>100%) and specific capacitance (260 F g-1). This work introduces IDTT-based polymers as bifunctional electro-optical materials for potential use in color-tailored, color-indicating, and self-regulating smart energy systems.

A complex structure of arrestin-2 bound to a G protein-coupled receptor.

Arrestins comprise a family of signal regulators of G-protein-coupled receptors (GPCRs), which include arrestins 1 to 4. While arrestins 1 and 4 are visual arrestins dedicated to rhodopsin, arrestins 2 and 3 (Arr2 and Arr3) are ß-arrestins known to regulate many nonvisual GPCRs. The dynamic and promiscuous coupling of Arr2 to nonvisual GPCRs has posed technical challenges to tackle the basis of arrestin binding to GPCRs. Here we report the structure of Arr2 in complex with neurotensin receptor 1 (NTSR1), which reveals an overall assembly that is strikingly different from the visual arrestin-rhodopsin complex by a 90° rotation of Arr2 relative to the receptor. In this new configuration, intracellular loop 3 (ICL3) and transmembrane helix 6 (TM6) of the receptor are oriented toward the N-terminal domain of the arrestin, making it possible for GPCRs that lack the C-terminal tail to couple Arr2 through their ICL3. Molecular dynamics simulation and crosslinking data further support the assembly of the Arr2‒NTSR1 complex. Sequence analysis and homology modeling suggest that the Arr2‒NTSR1 complex structure may provide an alternative template for modeling arrestin-GPCR interactions.

Ultralow surface energy self-assembled monolayers of iodo-perfluorinated alkanes on silica driven by halogen bonding.

Compact self-assembled monolayers (SAMs) of perfluorododecyl iodide (I-PFC12) of reproducible thickness (1.2 nm) are shown to form on silicon wafers. The SAMs have a high fluorine content (95%) and convey an extremely low surface energy to the silicon wafers (4.3 mN m-1), lower than previously reported in the literature for perfluorinated monolayers, and stable for over eight weeks. Shorter chain iodo-perfluorinated (I-PFC8) or bromo-perfluorinated molecules (Br-PFC10) led to less dense layers. The monolayers are stable to heating up to 60 °C, with some loss up to 150 °C. The I-PFC12 monolayer increases the work function of silicon wafers from 3.6 V to 4.4 eV, a factor that could be gainfully used in photovoltaic applications. The I-PFC12 monolayers can be transferred into patterns onto silica substrates by micro-contact printing. The NMR data and the reproducible thickness point to an upright halogen bonding interaction between the iodine in I-PFC12 and the surface oxygen on the native silica layer.

In situ recombination junction between p-Si and TiO2 enables high-efficiency monolithic perovskite/Si tandem cells.

Increasing the power conversion efficiency of silicon (Si) photovoltaics is a key enabler for continued reductions in the cost of solar electricity. Here, we describe a two-terminal perovskite/Si tandem design that increases the Si cell's output in the simplest possible manner: by placing a perovskite cell directly on top of the Si bottom cell. The advantageous omission of a conventional interlayer eliminates both optical losses and processing steps and is enabled by the low contact resistivity attainable between n-type TiO2 and Si, established here using atomic layer deposition. We fabricated proof-of-concept perovskite/Si tandems on both homojunction and passivating contact heterojunction Si cells to demonstrate the broad applicability of the interlayer-free concept. Stabilized efficiencies of 22.9 and 24.1% were obtained for the homojunction and passivating contact heterojunction tandems, respectively, which could be readily improved by reducing optical losses elsewhere in the device. This work highlights the potential of emerging perovskite photovoltaics to enable low-cost, high-efficiency tandem devices through straightforward integration with commercially relevant Si solar cells.

Influence of Moisture on the Energy-Level Alignment at the MoO3/Organic Interfaces.

MoO3 is widely used in polymer-based organic solar cells as an anode buffer layer because of its high workfunction and formation of a strong dipole at the MoO3/polymer interface facilitating charge transfer across the MoO3/polymer interface. In the present work, we show that exposure of the MoO3/polymer interface to moisture attracts water molecules to the interface via diffusion. Because of their own strong dipole, water molecules counter the dipole at the MoO3/polymer interface. As a consequence, the charge transfer across the MoO3/polymer will reduce and affect the charge transport across the interface. The outcome of this work thus suggests that it is critical to keep the MoO3/polymer interface moisture-free, which requires special precautions in device fabrications. The composition of the MoO3/P3HT:PC61BM interface is analyzed with X-ray photoelectron spectroscopy and the depth profiling technique, neutral impact collision ion scattering spectroscopy. The results show that the concentration of oxygen increases upon exposure but leaves the oxidation state of Mo unchanged. The valence electron spectroscopy technique shows that the dipole across the MoO3/P3HT:PC61BM interface decreases even for short-time exposure to atmosphere because of the diffusion of water molecules to the interface. The far-ranging consequences for organic electronic devices are discussed.

Cryo-EM structure of human rhodopsin bound to an inhibitory G protein.

G-protein-coupled receptors comprise the largest family of mammalian transmembrane receptors. They mediate numerous cellular pathways by coupling with downstream signalling transducers, including the hetrotrimeric G proteins Gs (stimulatory) and Gi (inhibitory) and several arrestin proteins. The structural mechanisms that define how G-protein-coupled receptors selectively couple to a specific type of G protein or arrestin remain unknown. Here, using cryo-electron microscopy, we show that the major interactions between activated rhodopsin and Gi are mediated by the C-terminal helix of the Gi α-subunit, which is wedged into the cytoplasmic cavity of the transmembrane helix bundle and directly contacts the amino terminus of helix 8 of rhodopsin. Structural comparisons of inactive, Gi-bound and arrestin-bound forms of rhodopsin with inactive and Gs-bound forms of the ß2-adrenergic receptor provide a foundation to understand the unique structural signatures that are associated with the recognition of Gs, Gi and arrestin by activated G-protein-coupled receptors.