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Rigidified heterocycles encompassing two dibenzo[b,f]oxazepine scaffolds and a 1,4-dihydropyrrolo[3,2-b]pyrrole core show intense blue emission and low turn-on voltage (≈3.5 V) in OLED devices.
The separation of rare-earth metals, vital for numerous advanced technologies, is hampered by their similar chemical properties, making ligand discovery a significant challenge. Traditional experimental and quantum chemistry approaches for identifying effective ligands are often resource-intensive. We introduce a machine learning protocol based on an equivariant neural network, Allegro, for the rapid and accurate prediction of binding energies in rare-earth complexes. Key to this work is our newly curated dataset of rare-earth metal complexes—made publicly available to foster further research—systematically generated using the Architector program. This dataset distinctively features functionalized derivatives of proven rare-earth-chelating scaffolds, hydroxypyridinone (HOPO), catecholamide (CAM), and their thio-analogues, selected for their established efficacy in binding these elements. Trained on this valuable resource, our Allegro models demonstrate excellent performance, particularly when trained to directly predict DFT-level binding energies, yielding highly accurate results that closely correlate with theoretical calculations on a diverse test set. Furthermore, this strategy exhibited strong out-of-sample generalization, accurately predicting binding energies for an isomeric HOPO-derivative ligand not seen during training. By substantially reducing computational demands, this machine learning framework, alongside the provided dataset, represent powerful tools to accelerate the high-throughput screening and rational design of novel ligands for efficient rare-earth metal separation.
Achieving cost-effective, sustainable solutions for large-scale energy storage are critical for advancing the global clean energy transition. In view of the challenges posed by limited lithium reserves, low-cost sodium-ion batteries (SIBs) have emerged as a promising direction, especially for grid-level energy storage. Among the various battery electrode materials, manganese dioxide (MnO 2 ) stands out as a favorable choice for such large-scale applications due to its earth abundance, cost-effectiveness, and non-toxic nature. Although MnO 2 is known as a pseudocapacitive material with superior cycling stability in aqueous electrolytes, its dissolution in non-aqueous electrolytes has restricted its use in long-lifetime batteries. In this study, we address two issues which have limited the use of MnO 2 electrodes in non-aqueous electrolytes. First, using electrochemical quartz crystal microbalance measurements in combination with other electrochemical methods, we demonstrate that diglyme (bis(2-methoxyethyl) ether) electrolyte can achieve stable cycling of electrodeposited ε-MnO 2 . These results enable us to tackle a second objective, that is increasing the mass loading of the MnO 2 electrode, since achieving high areal energy density is a significant factor in reducing manufacturing costs. Using 3D printed graphene aerogel (GA) as a scaffold, our studies show that the electrodeposited MnO 2 /GA electrodes possess scalable properties with mass loadings from 20 to 80 mg cm −2 . The resulting electrodes exhibit areal energy densities as high as 4.4 mA h cm −2 at a current density of 10 mA cm −2 . The high mass loaded MnO 2 electrodes were incorporated as a cathode in a SIB which used TiO 2 as the anode. The SIB device exhibited excellent performance with power densities in excess of 70 mW cm −2 . These studies highlight the promise of MnO 2 electrodes for use in a low-cost technology for large-scale energy storage.
Molecular excitons, which are excitations delocalized over multiple dyes in a wavelike manner, are of interest for a wide range of applications, including quantum information science. Numerous studies have templated a variety of synthetic dyes via a DNA scaffold to induce dye aggregation to create molecular excitons upon photoexcitation. Dye aggregate optical properties are critically dependent on relative dye geometry and local environment; therefore, an understanding of dye-dye and DNA-dye interactions is critical for advancing toward more complex DNA-dye systems. The extensively studied DNA Holliday junction (HJ) and less-studied double-crossover (DX) tile motif are fundamental test beds for designing complex and ultimately modular DNA-dye architectures. Here, we report the first study of single-linked squaraine dye aggregation and exciton delocalization on a larger and more stable (compared with the HJ) DX tile motif. We first highlight a few DNA-dye constructs that support single dyes and aggregates with distinct optical properties that are both tunable—through sample design, buffer conditions, and heat treatment—and robust to environment changes, including transfer to solid phase. Next, we assess several experimental and design considerations that demonstrate directed dye-driven assembly of a novel double-tile DNA configuration. Our results demonstrate that single-linked squaraine dyes templated to DX tiles provide a viable research path to design and evaluate dye aggregate networks that support exciton delocalization. We include herein the first report of exciton delocalization in the solid phase in a DNA-dye construct. Additionally, our findings indicate that dye aggregation impacts the assembly of the DNA-dye construct, and, in some cases, thereby cooperates with the DNA to determine a final robust system configuration. Finally, we show that a controlled annealing schedule can be employed to promote the homogeneous assembly of DNA-dye constructs. The findings in this study contribute to the understanding of DNA-dye systems and the relevant factors involved in their directed assembly to achieve specific constructs with desirable properties.
Lifetimes of photoexcited charge transfer (CT) states in transition metal chromophores are influenced by low-lying ligand field (LF) excited states, especially for 3d metal complexes. To manipulate interactions between LF and CT states, it is important to be able to control LF excited state energies using tunable synthetic variables. In this report, we use Fe 2p3d L 3 -edge resonant inelastic X-ray scattering (RIXS) to measure LF excited state energies of three homoleptic iron chromophores coordinated by strong-field N-heterocyclic carbenes (NHCs). We investigate the effect of oxidation state and ligand scaffold on LF energies and covalency parameters. A cyclometalated bis(NHC) ligand affords both high LF excited state energies (and thus high 10 Dq) as well as high metal–ligand covalency compared to other iron complexes with very strong-field ligands. However, for the set of complexes investigated, we do not observe meaningful correlation between the LF excited state energies and the CT excited state lifetimes. These results illustrate that targeting long-lived CT excited states necessitates control of multiple molecular excited state properties, with destabilization of the LF excited state energies proving necessary, but insufficient, to control the CT excited state lifetime in Fe carbene complexes.
Maximizing iridium utilization while maintaining high oxygen evolution reaction (OER) performance remains a persistent challenge in acidic water electrolysis. Immobilizing Ir on conductive, acid-stable supports is promising, yet simultaneously achieving sub-nanometer size, high area coverage, and strong electronic coupling is difficult. Here, we report a sequential surface synthesis on titanium nitride (TiN) that yields uniformly distributed sub-nanometer Ir arrays (∼0.7 nm). Our method uses ethylenediaminetetraacetic acid (EDTA) as a temporal scaffold: it chemisorbs to TiN to install dense chelating sites, captures Ir 3+ ions, and confines Ir cluster growth. A subsequent thermal treatment at 500 °C in a reducing atmosphere removes the ligand shell, while preserving ultrasmall particle size and establishing direct Ir–TiN electronic coupling. The optimized catalyst exhibits mixed Ir 0 /Ir x+ coordination with low charge-transfer resistance (R ct = 19.2 Ω), delivering a mass activity of 342 A g Ir −1 at 1.54 V in acidic electrolyte. In situ X-ray absorption spectroscopy reveals irreversible surface oxidation as the primary stability-limiting factor. This stepwise strategy provides a general framework for supported catalysts that maximize precious metal utilization via sub-nanometer dispersion.
Infective endocarditis (IE) is a cardiovascular disease often caused by bacteria of the viridans group of streptococci, which includes Streptococcus gordonii and Streptococcus sanguinis. Previous research has found that serine-rich repeat (SRR) proteins on the S. gordonii bacterial surface play a critical role in pathogenesis by facilitating bacterial attachment to sialylated glycans displayed on human platelets. Despite their important role in disease progression, there are currently no anti-adhesive drugs available on the market. Here, we performed structure-based virtual screening using an ensemble docking approach followed by consensus scoring to identify novel small molecule effectors against the sialoglycan binding domain of the SRR adhesin protein Hsa from the S. gordonii strain DL1. The screening successfully predicted nine compounds which were able to displace the native ligand (sialyl-T antigen) in an in vitro assay and bind competitively to Hsa. Furthermore, hierarchical clustering based on the MACCS fingerprints showed that eight of these small molecules do not share a common scaffold with the native ligand. This study indicates that SRR family of adhesin proteins can be inhibited by diverse small molecules and thus prevent the interaction of the protein with the sialoglycans. This opens new avenues for discovering potential drugs against IE.
Advancements in synthetic biology have facilitated the incorporation of heterologous metabolic pathways into various bacterial chassis, leading to the synthesis of targeted bioproducts. However, total output from heterologous production pathways can suffer from low flux, enzyme promiscuity, formation of toxic intermediates, or intermediate loss to competing reactions, which ultimately hinder their full potential. The self-assembling, easy-to-modify, protein-based bacterial microcompartments (BMCs) offer a sophisticated way to overcome these obstacles by acting as an autonomous catalytic module decoupled from the cell's regulatory and metabolic networks. More than a decade of fundamental research on various types of BMCs, particularly structural studies of shells and their self-assembly, the recruitment of enzymes to BMC shell scaffolds, and the involvement of ancillary proteins such as transporters, regulators, and activating enzymes in the integration of BMCs into the cell's metabolism, has significantly moved the field forward. These advances have enabled bioengineers to design synthetic multi-enzyme BMCs to promote ethanol or hydrogen production, increase cellular polyphosphate levels, and convert glycerol to propanediol or formate to pyruvate. These pioneering efforts demonstrate the enormous potential of synthetic BMCs to encapsulate non-native multi-enzyme biochemical pathways for the synthesis of high-value products.
This paper presents the design and evaluation of a lab-scale cable-driven parallel robot (CDPR) developed as a flexible platform for automated installation of prefabricated components onto exterior building envelopes. Traditional manual installation methods for prefabricated components, which depend on scaffolding, cranes, cherry pickers, and verbal coordination, are not only labor-intensive and error-prone but also face significant limitations in dense urban environments due to site access constraints. To address these challenges, we developed a lab-scale CDPR platform capable of autonomously transporting building envelope components from a designated pickup zone to their target installation location, minimizing the need for human intervention. This study describes the system’s mechanical design, actuation architecture, real-time feedback system, and control strategy of the CDPR, and evaluates its performance in a laboratory environment. The robot’s actuation system uses torque control for end-effector manipulation. The robot’s real-time pose feedback comes from a construction-grade total station and a wireless inertial measurement unit (IMU), which together support precise end-effector control. Experimental results demonstrate the successful integration of the hardware, sensing, state estimation, and control subsystems. Preliminary tests showed that our lab-scale prototype can position the end effector with an error of less than 3 mm, which is a level of precision not previously achieved by existing CDPRs in construction applications. The key findings are twofold: (1) torque-only control is necessary but not sufficient for minimizing final pose error, and (2) incorporating real-time pose feedback can achieve the desired placement accuracy.
Practical catalysts with a porous framework, such as zeolites, host catalytic reactions at active sites engrained in the pores and channels of the scaffold. The mechanism of interaction at these active sites, defining catalyst performance, remains elusive, in large part, due to the lack of surface characterization methods available for thick films or powders. Here, we present thin film analogs of practical catalysts that allow for the implementation of surface characterization tools, including advanced microscopy and operando spectroscopy methodologies. Specifically, we investigated bilayer silica, MFI nanosheets, and UiO-66 thin films using a multi-modal approach addressing film growth, characterization, and gas adsorption aimed at understanding catalytic activity, reactivity, and selectivity properties, as defined by molecular-level changes in the reaction mechanism.
Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.
Here we provide a detailed study of hydrogen bonding arrangements, relative stability, residual entropy, and an analysis of the many-body effects in the (H 2 O) 20 (D-cage), (H 2 O) 24 (T-cage), and (H 2 O) 28 (H-cage) hollow cages making up structures I (sI) and II (sII) of clathrate hydrate lattices. Based on the enumeration of the possible hydrogen bonding networks for a fixed oxygen atom scaffold, the residual entropy (S 0 ) of these three gas phase cages was estimated at 0.754 82, 0.754 44, and 0.754 17 · Nk b , where N is the number of molecules and k b is Boltzmann’s constant. A previously identified descriptor of enhanced stability based on the relative arrangement and connectivity of nearest-neighbor fragments on the polyhedral water cluster [strong-weak-effective-bond model] also applies to the larger hollow cages. The three cages contain a maximum of 7, 9, and 11 such preferable arrangements of trans nearest dimer pairs with one “free” OH bond on the donor molecule (t1d dimers). The Many-Body Expansion (MBE) up to the 4-body suggests that the many-body terms vary nearly linearly with the cluster binding energy. Using a hierarchical approach of screening the relative stability of networks starting from optimizations with the TIP4P, TTM2.1-F, and MB-pol classical potentials, subsequently refining at more accurate levels of electronic structure theory (DFT and MP2), and finally correcting for zero-point energy, we were able to identify a group of four low-lying isomers of the (H 2 O) 24 T-cage, two of which are antisymmetric and the other two form a pair of antipode configurations.
Photosynthetic organisms use pigment–protein complexes to capture the sunlight that powers most life on earth. Within these complexes, the position of the embedded pigments is all optimized for light harvesting. At the same time, the protein scaffold undergoes thermal fluctuations that vary the structure, and, thus, photophysics, of the complexes. While these variations are averaged out in ensemble measurements, single-molecule spectroscopy provides the ability to probe these conformational changes. We used single-molecule fluorescence spectroscopy to identify the photophysical substates reflective of distinct conformations and the associated conformational dynamics in phycoerythrin 545 (PE545), a pigment–protein complex from cryptophyte algae. Rapid switching between photophysical states was observed, indicating that ensemble measurements average over a conformational equilibrium. A highly quenched conformation was also identified, and its population increased under high light. This discovery establishes that PE545 has the characteristics to serve as a photoprotective site. Finally, unlike homologous proteins from the evolutionarily related cyanobacteria and red algae, quenching was not observed upon photobleaching, which may allow for robust photophysics without the need for rapid repair or replacement machinery. Collectively, these observations establish the presence of a rich and robust set of conformational states of PE545. Cryptophytes exhibit particularly diverse energetics owing to the variety of microenvironments in which they survive, and the conformational states and dynamics reported here may provide photophysical flexibility that contributes to their remarkable ability to flourish under diverse conditions.
Electrochemical water splitting is a key technology for a sustainable energy transition, providing a route to store surplus electricity from renewable sources. A central bottleneck is the sluggish oxygen evolution reaction (OER), which drives the search for catalysts that are active, stable, and inexpensive enough for large-scale deployment. Within this context, pure and doped NiO x H y combine high activity with low cost, making them prime candidates for alkaline OER. Yet, despite extensive study, the atomistic structure of NiOOH under operando conditions and the associated reaction mechanisms remain debated. Here, we investigate the structural complexity of pure β-NiOOH, the scaffold for its doped derivatives. We systematically investigate the oxidation of the surface adsorbates via proton-coupled electron transfer steps across relevant facets and sites, identifying the most probable sequence of deprotonation events. Our results reveal asymmetric charge accumulation on Wulff-relevant surfaces and show how applied potential can promote morphological restructuring. Explicit solvation is included through machine-learning interatomic potential molecular dynamics of the NiOOH/water interface, which allows us to resolve the hydrophobic and hydrophilic character of different surfaces and the associated interfacial water structure. Together, these insights demonstrate how surface chemistry and solvation jointly govern the stability of NiOOH and the accumulation of surface charge, with possible implications for catalytic performance.
Xeroderma pigmentosum group G (XPG) protein is both a functional partner in multiple DNA damage responses (DDR) and a pathway coordinator and structure-specific endonuclease in nucleotide excision repair (NER). Different mutations in the XPG gene ERCC5 lead to either of two distinct human diseases: Cancer-prone xeroderma pigmentosum (XP-G) or the fatal neurodevelopmental disorder Cockayne syndrome (XP-G/CS). To address the enigmatic structural mechanism for these differing disease phenotypes and for XPG’s role in multiple DDRs, here we determined the crystal structure of human XPG catalytic domain (XPGcat), revealing XPG-specific features for its activities and regulation. Furthermore, XPG DNA binding elements conserved with FEN1 superfamily members enable insights on DNA interactions. Notably, all but one of the known pathogenic point mutations map to XPGcat, and both XP-G and XP-G/CS mutations destabilize XPG and reduce its cellular protein levels. Mapping the distinct mutation classes provides structure-based predictions for disease phenotypes: Residues mutated in XP-G are positioned to reduce local stability and NER activity, whereas residues mutated in XP-G/CS have implied long-range structural defects that would likely disrupt stability of the whole protein, and thus interfere with its functional interactions. Combined data from crystallography, biochemistry, small angle X-ray scattering, and electron microscopy unveil an XPG homodimer that binds, unstacks, and sculpts duplex DNA at internal unpaired regions (bubbles) into strongly bent structures, and suggest how XPG complexes may bind both NER bubble junctions and replication forks. Collective results support XPG scaffolding and DNA sculpting functions in multiple DDR processes to maintain genome stability.
Significance Gas separation membranes are an emerging energy-efficient alternative toward conventional, energy-intensive separation technologies such as cryogenic distillation. Ladder polymers with intrinsic microporosity show exceptional promise toward redefining state-of-the-art gas separation membranes due to their high permeability (throughput) and selectivity (separation efficiency). However, they are typically inhibited by major reductions in permeability over time due to collapsing membrane free volume (open space between polymer chains), forfeiting their greatest asset. This work explores a route toward enhanced aging resistance and overall separation performance by incorporating pentiptycene (an H-shaped scaffold containing five fused arene rings) into ladder-like polymers to incorporate natural, more permanent “micropores” that aren’t susceptible to densification of polymer chains that occurs over time in traditional microporous polymers.
Significance Phytochromes are well-known far-red-light sensors found in plants that trigger adaptive responses to facilitate competition for light capture with neighboring plants. Red- and far-red sensing are also critical for cyanobacteria living in the far-red–enriched shade of plants. This work reports the crystal structure of a far-red–sensing cyanobacteriochrome, a distant cyanobacterial relative of phytochrome. These studies shed insights into the molecular basis of far-red-sensing by phycobilin-based photoreceptors. Owing to the deep tissue penetration of far-red light, far-red–sensing cyanobacteriochromes are promising protein scaffolds for developing genetically encoded photoswitches, optoacoustic contrast agents, and fluorescent probes for in situ imaging and optogenetic applications.
Two independent structures of the proton-pumping, respiratory cytochrome bo3 ubiquinol oxidase (cyt bo 3 ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene–maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme b, heme o 3 , and Cu B ), the redox-active cross-linked histidine–tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome c oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75I and R71 I . In both structures, residue H98 I occupies two conformations. In conformation 1, H98 I forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98 I has flipped to form a hydrogen bond with E14 I at the N-terminal end of TM0. We propose that H98 I dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98 I .