MnFe Prussian Blue Analogue Open Cages for Sodium-Ion Batteries: Simultaneous Evolution of Structure, Morphology, and Energy Storage Properties.

Prussian blue analogues (PBAs) exhibiting hollow morphologies have garnered considerable attention owing to their remarkable electrochemical properties. In this study, a one-pot strategy is proposed for the synthesis of MnFe PBA open cages. The materials are subsequently employed as cathode electrode in sodium-ion batteries (SIBs). The simultaneous evolution of structure, morphology, and performance during the synthesis process is investigated. The findings reveal substantial structural modifications as the reaction time is prolonged. The manganese content in the samples diminishes considerably, while the potassium content experiences an increase. This compositional variation is accompanied by a significant change in the spin state of the transition metal ions. These structural transformations trigger the occurrence of the Kirkendall effect and Oswald ripening, culminating in a profound alteration of the morphology of MnFe PBA. Moreover, the shifts in spin states give rise to distinct changes in their charge-discharge profiles and redox potentials. Furthermore, an exploration of the formation conditions of the samples and their variations before and after cycling is conducted. This study offers valuable insights into the intricate relationship between the structure, morphology, and electrochemical performance of MnFe PBA, paving the way for further optimizations in this promising class of materials for energy storage applications.

Understanding the Poly (Triazine Imide) Crystals Formation Process: The Conversion from Heptazine to Triazine.

Poly (triazine imide) (PTI) generally obtained via ionothermal synthesis features extended π-conjugation and enhanced crystallinity. However, in-depth investigation of the polycondensation process for PTI is an onerous task due to multiple influencing factors and limited characterization techniques. Herein, to simplify the polymerization route and exclude non-essential factors, PTI was prepared by calcining only melamine and LiCl. This study aims to identify the pivotal role of LiCl in PTI formation, which can convert heptazine-based intermediates into more stable triazine-based PTI framework. Based on this discovery, we demonstrate the transformation process of the prepared samples from amorphous Bulk g-C3 N4 to regular PTI, and further prove that the reaction with LiCl causes disruption of heptazine covalent organic frameworks. Additionally, the PTI exhibits higher photocatalytic water splitting performance due to efficient charge carrier mobility and separation, as well as faster reaction kinetics. This discovery deepens understanding of the polycondensation process of PTI crystals and provides insights toward the rational design of crystalline carbon nitride-based semiconductors.

Structure Evolution of Iron (Hydr)oxides under Nanoconfinement and Its Implication for Water Treatment.

In the development of nanoenabled technologies for large-scale water treatment, immobilizing nanosized functional materials into the confined space of suitable substrates is one of the most effective strategies. However, the intrinsic effects of nanoconfinement on the decontamination performance of nanomaterials, particularly in terms of structural modulation, are rarely unveiled. Herein, we investigate the structure evolution and decontamination performance of iron (hydr)oxide nanoparticles, a widely used material for water treatment, when confined in track-etched (TE) membranes with channel sizes varying from 200 to 20 nm. Nanoconfinement drives phase transformation from ferrihydrite to goethite, rather than to hematite occurring in bulk systems, and the increase in the nanoconfinement degree from 200 to 20 nm leads to a significant drop in the fraction of the goethite phase within the aged products (from 41% to 0%). The nanoconfinement configuration is believed to greatly slow down the phase transformation kinetics, thereby preserving the specific adsorption of ferrihydrite toward As(V) even after 20-day aging at 343 K. This study unravels the structure evolution of confined iron hydroxide nanoparticles and provides new insights into the temporospatial effects of nanoconfinement on improving the water decontamination performance.

Targeted Stimulation of Micropores by CS2 Extraction on Molecular of Coal.

The targeted stimulation of micropores based on the transformation of coal's molecular structure is proposed due to the chemical properties and difficult-to-transform properties of micropores. Carbon disulfide (CS2) extraction is used as a targeted stimulation to reveal the internal evolution mechanism of micropore transformation. The variations of microcrystalline structures and micropores of bituminous coal and anthracite extracted by CS2 were analyzed with X-ray diffraction (XRD), low-temperature carbon dioxide (CO2) adsorption, and molecular simulation. The results show that CS2 extraction, with the broken chain effect, swelling effect, and aromatic ring rearrangement effect, can promote micropore generation of bituminous coal by transforming the microcrystalline structure. Furthermore, CS2 extraction on bituminous coal can decrease the average micropore size and increase the micropore volume and area. The aromatic layer fragmentation effect of CS2 extraction on anthracite, compared to the micropore generation effect of the broken chain effect and swelling effect, can enlarge micropores more remarkably, as it induces an enhancement in the average micropore size and a decline in the micropore volume and area. The research is expected to provide a theoretical basis for establishing reservoir stimulation technology based on CS2 extraction.

In situ/Operando Synchrotron Radiation Analytical Techniques for CO2/CO Reduction Reaction: From Atomic Scales to Mesoscales.

Electrocatalytic carbon dioxide/carbon monoxide reduction reaction (CO(2)RR) has emerged as a prospective and appealing strategy to realize carbon neutrality for manufacturing sustainable chemical products. Developing highly active electrocatalysts and stable devices has been demonstrated as effective approach to enhance the conversion efficiency of CO(2)RR. In order to rationally design electrocatalysts and devices, a comprehensive understanding of the intrinsic structure evolution within catalysts and micro-environment change around electrode interface, particularly under operation conditions, is indispensable. Synchrotron radiation has been recognized as a versatile characterization platform, garnering widespread attention owing to its high brightness, elevated flux, excellent directivity, strong polarization and exceptional stability. This review systematically introduces the applications of synchrotron radiation technologies classified by radiation sources with varying wavelengths in CO(2)RR. By virtue of in situ/operando synchrotron radiationanalytical techniques, we also summarize relevant dynamic evolution processes from electronic structure, atomic configuration, molecular adsorption, crystal lattice and devices, spanning scales from the angstrom to the micrometer. The merits and limitations of diverse synchrotron characterization techniques are summarized, and their applicable scenarios in CO(2)RR are further presented. On the basis of the state-of-the-art fourth-generation synchrotron facilities, a perspective for further deeper understanding of the CO(2)RR process using synchrotron radiation analytical techniques is proposed.

WITHDRAWN: NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750.

This article was initially published in the Journal of Structural Biology, instead of the Journal of Structural Biology: X, due to a publisher error. We regret the inconvenience. The link to the article published in Journal of Structural Biology: X is presented below: https://www.sciencedirect.com/science/article/pii/S2590152423000090. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/policies/article-withdrawal.

Approaching Elaborate Control of the Nano-Products of Carbothermal Reduction Reaction Through In Situ Identification.

Atomic understanding of a chemical reaction can realize the programmable design and synthesis of desired products with specific compositions and structures. Through directly monitoring the phase transition and tracking the dynamic evolution of atoms in a chemical reaction, in situ transmission electron microscopy (TEM) techniques offer the feasibility of revealing the reaction kinetics at the atomic level. Nevertheless, such investigation is quite challenging, especially for reactions involving multi-phase and complex interfaces, such as the widely adopted carbothermal reduction (CTR) reactions. Herein, in-situ TEM is applied to monitor the CTR of Co3 O4 nanocubes on reduced graphene oxide nanosheets. Together with the first-principle calculation, the migration route of Co atoms during the phase transition of the CTR reaction is revealed. Meanwhile, the interfacial edge-dislocations/stress-gradient is identified as a result of the atomistic diffusion, which in turn can affect the morphology variation of the reactants. Accordingly, controllable synthesis of Co-based nanostructure with a desirable phase and structure has been achieved. This work not only provides atomic kinetic insight into CTR reactions but also offers a novel strategy for the design and synthesis of functional nanostructures for emerging energy technologies.

Four New Sb-based Orthophosphates: Cation Regulation to Investigate Diversified Structural Architecture.

In the work, four new Sb-based phosphates, K4 (SbO2 )5 (PO4 )3 , Rb(SbO2 )2 PO4 , Rb3 (SbO2 )3 (PO4 )2 and Cs3 (SbO2 )3 (PO4 )2 (H2 O)1.32 , were successfully synthesized by a high-temperature melt method. Among them, Rb(SbO2 )2 PO4 and Rb3 (SbO2 )3 (PO4 )2 are the first reported examples of Rb-containing alkali metal Sb-based phosphates. They show three-dimensional (3D) frameworks composed of [Sb8 P4 O30 ]∞ layer for K4 (SbO2 )5 (PO4 )3 and [Sb6 P2 O20 ]∞ layer for Rb(SbO2 )2 PO4 , and 2D lamellar structure composed of [Sb3 P2 O10 ]∞ for Rb3 (SbO2 )3 (PO4 )2 and Cs3 (SbO2 )3 (PO4 )2 (H2 O)1.32 . A detailed structural comparison shows that the structure dimensions for them transfer from 1D to complex 3D framework with the increase of (Sb+P)/O ratio, which affects performances of the compounds. Optical property and energy band structure calculations were also carried out based on the density functional theory (DFT). The present study enriches the diversity of Sb-based phosphates and paves the way for further explore their optical properties in the future.

Monitoring Electron Flow in Nickel Single-Atom Catalysts during Nitrogen Photofixation.

An efficient catalytic system for nitrogen (N2) photofixation generally consists of light-harvesting units, active sites, and an electron-transfer bridge. In order to track photogenerated electron flow between different functional units, it is highly desired to develop in situ characterization techniques with element-specific capability, surface sensitivity, and detection of unoccupied states. In this work, we developed in situ synchrotron radiation soft X-ray absorption spectroscopy (in situ sXAS) to probe the variation of electronic structure for a reaction system during N2 photoreduction. Nickel single-atom and ceria nanoparticle comodified reduced graphene oxide (CeO2/Ni-G) was designed as a model catalyst. In situ sXAS directly reveals the dynamic interfacial charge transfer of photogenerated electrons under illumination and the consequent charge accumulation at the catalytic active sites for N2 activation. This work provides a powerful tool to monitor the electronic structure evolution of active sites under reaction conditions for photocatalysis and beyond.

Bi2O3/BiO2 Nanoheterojunction for Highly Efficient Electrocatalytic CO2 Reduction to Formate.

Heterostructure engineering plays a vital role in regulating the material interface, thus boosting the electron transportation pathway in advanced catalysis. Herein, a novel Bi2O3/BiO2 heterojunction catalyst was synthesized via a molten alkali-assisted dealumination strategy and exhibited rich structural dynamics for an electrocatalytic CO2 reduction reaction (ECO2RR). By coupling in situ X-ray diffraction and Raman spectroscopy measurements, we found that the as-synthesized Bi2O3/BiO2 heterostructure can be transformed into a novel Bi/BiO2 Mott-Schottky heterostructure, leading to enhanced adsorption performance for CO2 and *OCHO intermediates. Consequently, high selectivity toward formate larger than 95% was rendered in a wide potential window along with an optimum partial current density of -111.42 mA cm-2 that benchmarked with the state-of-the-art Bi-based ECO2RR catalysts. This work reports the construction and fruitful structural dynamic insights of a novel heterojunction electrocatalyst for ECO2RR, which paves the way for the rational design of efficient heterojunction electrocatalysts for ECO2RR and beyond.

The archaeal triphosphate tunnel metalloenzyme SaTTM defines structural determinants for the diverse activities in the CYTH protein family.

CYTH proteins make up a large superfamily that is conserved in all three domains of life. These enzymes have a triphosphate tunnel metalloenzyme (TTM) fold, which typically results in phosphatase functions, e.g., RNA triphosphatase, inorganic polyphosphatase, or thiamine triphosphatase. Some CYTH orthologs cyclize nucleotide triphosphates to 3',5'-cyclic nucleotides. So far, archaeal CYTH proteins have been annotated as adenylyl cyclases, although experimental evidence to support these annotations is lacking. To address this gap, we characterized a CYTH ortholog, SaTTM, from the crenarchaeote Sulfolobus acidocaldarius. Our in silico studies derived ten major subclasses within the CYTH family implying a close relationship between these archaeal CYTH enzymes and class IV adenylyl cyclases. However, initial biochemical characterization reveals inability of SaTTM to produce any cyclic nucleotides. Instead, our structural and functional analyses show a classical TTM behavior, i.e., triphosphatase activity, where pyrophosphate causes product inhibition. The Ca2+-inhibited Michaelis complex indicates a two-metal-ion reaction mechanism analogous to other TTMs. Cocrystal structures of SaTTM further reveal conformational dynamics in SaTTM that suggest feedback inhibition in TTMs due to tunnel closure in the product state. These structural insights combined with further sequence similarity network-based in silico analyses provide a firm molecular basis for distinguishing CYTH orthologs with phosphatase activities from class IV adenylyl cyclases.

From ß-Na2 B6 O10 to Na3 AlB8 O15 and Na3 Al2 B7 O15 : Structural Tuning of Anionic-Group Architectures by Substitution of [BO4 ] by [AlO4 ] Covalent Tetrahedra.

Two new sodium aluminum borates, Na3 AlB8 O15 and Na3 Al2 B7 O15 , have been successfully synthesized by the high-temperature solution method. They crystallize in the different space groups, P21 /c and P2/c, respectively. The B-O configurations of ß-Na2 B6 O10 , Na3 AlB8 O15 and Na3 Al2 B7 O15 are compared to feature complicated different dimensional open-framework structures caused by the substitution of [BO4 ] by [AlO4 ] covalent tetrahedra. Moreover, the experimental results indicate that Na3 AlB8 O15 and Na3 Al2 B7 O15 have short ultraviolet (UV) cutoff edges (<187 nm). The first-principles calculations show that Na3 AlB8 O15 and Na3 Al2 B7 O15 have moderate birefringence (0.075 and 0.041@1064 nm, respectively).

Designing Quinone-Based Anodes with Rapid Kinetics for Rechargeable Proton Batteries.

Quinone compounds, which are capable of accommodating proton (H+ ), are emerging electrodes in aqueous batteries. However, the storage mechanism of proton in quinone compounds is less known and the energy/power density of quinone-based proton battery is still limited. Here we design a series of quinone anodes and study their electrochemical properties in acidic electrolyte, in which tetramethylquinone (TMBQ) delivers a high capacity of 300 mAh g-1 with an extremely low polarization of 20 mV at 1 C, and maintains over 50 % theoretical capacity in less than 16 seconds. The fast kinetics of TMBQ is attributed to the continuous H+ migration channel, high H+ diffusion coefficient (10-6  cm2 s-1 ), and low H+ migration energy barrier (0.26 eV). When coupling with MnO2 cathode, the battery shows a long lifespan of 4000 cycles with a capacity retention of 77 % at 5 C. This study reveals the proton transport in quinone-electrodes and offers new insights to design advanced aqueous batteries.

The Crucial Role of Electrode Potential of a Working Anode in Dictating the Structural Evolution of Solid Electrolyte Interphase.

The performance of rechargeable lithium (Li) batteries is highly correlated with the structure of solid electrolyte interphase (SEI). The properties of a working anode are vital factors in determining the structure of SEI; however, the correspondingly poor understanding hinders the rational regulation of SEI. Herein, the electrode potential and anode material, two critical properties of an anode, in dictating the structural evolution of SEI were investigated theoretically and experimentally. The anode potential is identified as a crucial role in dictating the SEI structure. The anode potential determines the reduction products in the electrolyte, ultimately giving rise to the mosaic and bilayer SEI structure at high and low potential, respectively. In contrast, the anode material does not cause a significant change in the SEI structure. This work discloses the crucial role of electrode potential in dictating SEI structure and provides rational guidance to regulate SEI structure.

Detecting Signatures of Positive Selection against a Backdrop of Compensatory Processes.

There are known limitations in methods of detecting positive selection. Common methods do not enable differentiation between positive selection and compensatory covariation, a major limitation. Further, the traditional method of calculating the ratio of nonsynonymous to synonymous substitutions (dN/dS) does not take into account the 3D structure of biomacromolecules nor differences between amino acids. It also does not account for saturation of synonymous mutations (dS) over long evolutionary time that renders codon-based methods ineffective for older divergences. This work aims to address these shortcomings for detecting positive selection through the development of a statistical model that examines clusters of substitutions in clusters of variable radii. Additionally, it uses a parametric bootstrapping approach to differentiate positive selection from compensatory processes. A previously reported case of positive selection in the leptin protein of primates was reexamined using this methodology.

Ferric iron stimulation in marine SMFCs: Impact on the microbial structure evolution in contaminated sediments with low and high molecular weight PAHs.

The impact of ferric iron stimulation on the evolution of microbial structure in marine sediment microbial fuel cells (SMFCs), operated for the bioremediation of a complex mixture of low and high molecular weight PAHs (naphthalene, fluorene, pyrene and benzo(a)pyrene), was assessed. Microbial evolution profiles showed high relative abundances of exoelectrogenic iron-reducing bacteria throughout the biodegradation, namely Geoalkalibacter, under ferric iron stimulation and anode reducing conditions, irrespective of sulfate reducing bacteria (SRB) inhibition. Highest PAHs removal was measured in the absence of anode reduction, under Fe stimulation and SRB inhibition, reaching 40.85% for benzo(a)pyrene, the most persistent PAH used in this study. Results suggest that amendment of contaminated sediment with ferric iron could constitute a better bioremediation strategy than using SMFCs. This becomes significant when considering the well-established and dominant indigenous SRB population in marine sediments that usually limits the performance of the anode as a terminal electron acceptor in marine SMFCs.

Carboranealkynyl-Protected Gold Nanoclusters: Size Conversion and UV/Vis-NIR Optical Properties.

Structure evolution has become an effective way to assemble novel monolayer-protected metal nanomolecules. However, evolution with alkynyl-stabilized metal clusters still remains rarely explored. Herein, we present a carboranealkynyl-protected gold nanocluster [Au28 (C4 B10 H11 )12 (tht)8 ]3+ (Au28 , tht=tetrahydrothiophene) possessing an open-shell electronic structure with 13 free electrons, which was isolated by a facile self-reduction method with 9-HC≡C-closo-1,2-C2 B10 H11 as the two-in-one reducing and protecting agent. Notably, Au28 undergoes a complete transformation in methanol into a stable and smaller-sized nanocluster [Au23 (C4 B10 H11 )9 (tht)6 ]2+ (Au23 ) bearing 12 valence electrons and crystal-field-like split superatomic 1D orbitals. The transformation process was systematically monitored with ESI-MS and UV/Vis absorption spectra. Au28 and Au23 both display optical absorption covering the UV/Vis-NIR range and NIR emission, which facilitates their potential application in the biomedical and photocatalytic fields.

The Molecular Clock in the Evolution of Protein Structures.

The molecular clock hypothesis, which states that substitutions accumulate in protein sequences at a constant rate, plays a fundamental role in molecular evolution but it is violated when selective or mutational processes vary with time. Such violations of the molecular clock have been widely investigated for protein sequences, but not yet for protein structures. Here, we introduce a novel statistical test (Significant Clock Violations) and perform a large scale assessment of the molecular clock in the evolution of both protein sequences and structures in three large superfamilies. After validating our method with computer simulations, we find that clock violations are generally consistent in sequence and structure evolution, but they tend to be larger and more significant in structure evolution. Moreover, changes of function assessed through Gene Ontology and InterPro terms are associated with large and significant clock violations in structure evolution. We found that almost one third of significant clock violations are significant in structure evolution but not in sequence evolution, highlighting the advantage to use structure information for assessing accelerated evolution and gathering hints of positive selection. Clock violations between closely related pairs are frequently significant in sequence evolution, consistent with the observed time dependence of the substitution rate attributed to segregation of neutral and slightly deleterious polymorphisms, but not in structure evolution, suggesting that these substitutions do not affect protein structure although they may affect stability. These results are consistent with the view that natural selection, both negative and positive, constrains more strongly protein structures than protein sequences. Our code for computing clock violations is freely available at https://github.com/ugobas/Molecular_clock.

Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects.

BACKGROUND: Drosophila subobscura has long been a central model in evolutionary genetics. Presently, its use is hindered by the lack of a reference genome. To bridge this gap, here we used PacBio long-read technology, together with the available wealth of genetic marker information, to assemble and annotate a high-quality nuclear and complete mitochondrial genome for the species. With the obtained assembly, we performed the first synteny analysis of genome structure evolution in the subobscura subgroup. RESULTS: We generated a highly-contiguous ~ 129 Mb-long nuclear genome, consisting of six pseudochromosomes corresponding to the six chromosomes of a female haploid set, and a complete 15,764 bp-long mitogenome, and provide an account of their numbers and distributions of codifying and repetitive content. All 12 identified paracentric inversion differences in the subobscura subgroup would have originated by chromosomal breakage and repair, with some associated duplications, but no evidence of direct gene disruptions by the breakpoints. Between lineages, inversion fixation rates were 10 times higher in continental D. subobscura than in the two small oceanic-island endemics D. guanche and D. madeirensis. Within D. subobscura, we found contrasting ratios of chromosomal divergence to polymorphism between the A sex chromosome and the autosomes. CONCLUSIONS: We present the first high-quality, long-read sequencing of a D. subobscura genome. Our findings generally support genome structure evolution in this species being driven indirectly, through the inversions' recombination-suppression effects in maintaining sets of adaptive alleles together in the face of gene flow. The resources developed will serve to further establish the subobscura subgroup as model for comparative genomics and evolutionary indicator of global change.