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Cation size primarily governs dynamic correlations in aqueous solutions. However, drawing a clear line between chaotropic and cosmotrope ions is complicated by the fact that all cations delay dynamic correlation decay.
Bacterial microcompartments (BMCs) are polyhedral structures that segregate enzymatic cargo from the cytosol via encapsulation within a protein shell. Unlike other biological polyhedra, such as viral capsids and encapsulins, BMC shells can exhibit a highly advantageous structural and functional plasticity, conforming to a variety of anabolic (CO 2 fixation in carboxysomes) and catabolic (nutrient assimilation in metabolosomes) roles. Consequently, understanding the subunit properties and associated protein–protein interaction processes that guide shell assembly and function is a necessary step to fully harness BMCs as modular, biotechnological nanomachines. Here, we describe the recent insights into the dynamics of structural features of the key BMC domain (Pfam00936)-containing proteins, which serve as a structural template for BMC-H and BMC-T shell building blocks.
Chemical and conformational changes are crucial to protein function and its pharmacological control. X-ray crystallography can reveal these changes in atomic detail, but standard analysis methods, which refine separate datasets, often overlook differences that are subtle or arise in only a subset of molecules. Direct comparison of crystallographic datasets is, in principle, more powerful, but systematic errors (“scales”) often mask changes in the crystallographic observables (“structure factors”). Machine learning algorithms that jointly estimate scales and structure factors can address this limitation. Here, we augment this approach with multivariate, structured priors derived from crystallographic theory, implemented in the variational deep learning framework Careless. Doing so strongly improves the detection of protein dynamics, element-specific anomalous signals, and the binding of drug candidates, offering a robust approach to comparative crystallography and, potentially, to detection of protein dynamics by other structure determination methods.
The constant fragment (Fc) of the immunoglobulin G1 (IgG1) subtype is increasingly recognized as a crucial scaffold in the development of advanced therapeutics due to its enhanced specificity, efficacy, and extended half‐life. A prime example is VEGF‐Trap (Aflibercept), a recombinant fusion protein that merges the Fc region of the IgG1 subtype with the binding domains of vascular endothelial growth factor receptors (VEGFR)‐1 and VEGFR‐2. The Fc region's role in N‐glycosylation is particularly important, as it significantly influences protein stability. Herein, the first near‐physiological temperature structures of the N‐glycan‐bound Fc fragment of IgG1 subtype from a biosimilar VEGF‐Trap are presented, determined using the SPring‐8 Angstrom Compact free electron LAser (SACLA) and the Turkish Light Source (Turkish DeLight). Comparative analysis with cryogenic structures, including existing data, reveals alternate conformations within the glycan‐binding pocket. Furthermore, molecular dynamics simulations indicate the presence of a high degree of structural plasticity, explaining how the protein adapts its structure through conformational changes. The observed structural fluctuations/conformational changes demonstrate the effect of N‐glycans on protein stability. These findings offer new insights into the molecular basis of Fc‐mediated functions and provide valuable information for the design of next‐generation therapeutics.
The structural evolution of spin crossover (SCO) complexes during their spin transition at equilibrium and out-of-equilibrium conditions needs to be understood to enable their successful utilisation in displays, actuators and memory components. In this study, diffraction techniques were employed to study the structural changes accompanying the temperature increase and the light irradiation of a defect [2 × 2] triiron(II) metallogrid of the form [Fe II 3 L H 2 (HL H ) 2 ](BF 4 ) 4 ·4MeCN (FE3), L H = 3,5-bis{6-(2,2'-bipyridyl)}pyrazole. Although a multi-temperature crystallographic investigation on single crystals evidenced that the compound does not exhibit a thermal spin transition, the structural analysis of the defect grid suggests that the flexibility of the grid, provided by a metal-devoid vertex, leads to interesting characteristics that can be used for intermolecular cooperativity in related thermally responsive systems. Time-resolved photocrystallography results reveal that upon excitation with a ps laser pulse, the defect grid shows the first two steps of the out-of-equilibrium process, namely the photoinduced and elastic steps, occurring at the ps and ns time scales, respectively. Similar to a previously reported [2 × 2] tetrairon(II) metallogrid, FE3 exhibits a local distortion of the entire grid during the photoinduced step and a long-range distortion of the lattice during the elastic step. Although the lifetime of the pure photoinduced high spin (HS) state is longer in the tetranuclear grid than in the defect grid, suggesting that the global nuclearity plays a crucial role for the lifetime of the photoinduced species, the influence of the co-crystalising solvent on the lifetime of the photoinduced HS state remains unknown. This study sheds light on the out-of-equilibrium dynamics of a thermally silent defect triiron SCO metallogrid.
Abstract Amorphous carbon (a-C) has attracted considerable interest due to its desirable properties, which are strongly dependent on its structure, density and impurities. Using ab initio molecular dynamics simulations we show that the sp 2 /sp 3 content and underlying structural order of a-C produced via liquid quenching evolve at high temperatures and pressures on sub-nanosecond timescales. Graphite-like densities ( $$\lesssim$$ ≲ 2.7 g/cc) favor the formation of layered arrangements characterized by sp 2 disordered bonding resembling recently synthesized monolayer amorphous carbon (MAC), while at diamond-like densities ( $$\gtrsim$$ ≳ 3.3 g/cc) the resulting structures are dominated by disordered tetrahedral sp 3 hybridization typical of diamond-like amorphous carbon (DLC). At intermediate densities the system is a highly compressible mixture of coexisting sp 2 and sp 3 regions that continue to segregate over 10’s of picoseconds. The addition of nitrogen (20.3%) (a-CN) generates major system features similar with those of a-C, but has the unexpected effect of reinforcing the thermodynamically disfavored carbon structural motifs at low and high densities, while inhibiting phase separation in the intermediate region. At the same time, no nitrogen elimination from the carbon framework is observed above $$\simeq$$ ≃ 2.8 g/cc, suggesting that nitrogen impurities are likely to remain embedded in the carbon structures during fast temperature quenches at high pressures.
The lack of model single-atom catalysts (SACs) and atomic-resolution operando spectroscopic techniques greatly limits our comprehension of the nature of catalysis. Herein, based on the designed model single-Fe-atom catalysts with well-controlled microenvironments, we have explored the exact structure of catalytic centers and provided insights into a spin-crossover-involved mechanism for oxygen reduction reaction (ORR) using operando Raman, X-ray absorption spectroscopies, and the developed operando 57 Fe Mössbauer spectroscopy. In combination with theoretical studies, the N-FeN 4 C 10 moiety is evidenced as a more active site for ORR. Moreover, the potential-relevant dynamic cycles of both geometric structure and electronic configuration of reactive single-Fe-atom moieties are evidenced via capturing the peroxido (*O 2 -) and hydroxyl (*OH-) intermediates under in situ ORR conditions. Overall, we anticipate that the integration of operando techniques and SACs in this work shall shed some light on the electronic-level insight into the catalytic centers and underlying reaction mechanism.
A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods—UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.
As countries accelerate their energy transitions, understanding how renewable energy (RE) systems structurally integrate into national economies is essential. This study presents a longitudinal economic input-output (EIO) analysis of the renewable energy sector in South Korea from 2016 to 2022. We develop a novel EIO-based framework that disaggregates the RE sector both by energy source (thermal, hydro, nuclear and renewable) and by industrial function (manufacturing, generation, and services), allowing for a detailed assessment of production dynamics, value-added creation, and import dependency. By quantifying backward and forward linkages and induced economic effects, the analysis reveals persistent structural vulnerabilities in renewable manufacturing and increasing sectoral interdependencies. Results reveal that while the renewable energy sector's production and value-added shares have increased, critical segments remain highly import-dependent, particularly in equipment manufacturing. The analysis highlights systemic gaps in domestic supply chain resilience and offers sector-specific insights for reducing vulnerability and enhancing energy security. Although applied to South Korea as a case study, the proposed framework is designed to be transferable to other national contexts where renewable energy planning requires economic structural insights. The findings offer policy-relevant guidance for enhancing domestic energy resilience and aligning industrial strategy with long-term decarbonization goals.
Abstract Because of their high photon flux, x-ray free-electron lasers (FEL) allow to resolve the structure of individual nanoparticles via coherent diffractive imaging (CDI) within a single x-ray pulse. Since the inevitable rapid destruction of the sample limits the achievable resolution, a thorough understanding of the spatiotemporal evolution of matter on the nanoscale following the irradiation is crucial. We present a technique to track x-ray induced structural changes in time and space by recording two consecutive diffraction patterns of the same single, free-flying nanoparticle, acquired separately on two large-area detectors opposite to each other, thus examining both the initial and evolved particle structure. We demonstrate the method at the extreme ultraviolet (XUV) and soft x-ray Free-electron LASer in Hamburg (FLASH), investigating xenon clusters as model systems. By splitting a single XUV pulse, two diffraction patterns from the same particle can be obtained. For focus intensities of about 2 × 10 12 W cm −2 we observe still largely intact clusters even at the longest delays of up to 650 picoseconds of the second pulse, indicating that in the highly absorbing systems the damage remains confined to one side of the cluster. Instead, in case of five times higher flux, the diffraction patterns show clear signatures of disintegration, namely increased diameters and density fluctuations in the fragmenting clusters. Future improvements to the accessible range of dynamics and time resolution of the approach are discussed.
3D printing is an emerging technology for the fabrication of energy storage devices, offering advantages over traditional manufacturing methods. However, optimization and design of such devices requires an understanding of the meso-structure formation during the 3D printing process. This study utilizes operando coherent X-ray scattering, X-ray Photon Correlation Spectroscopy (XPCS), to study the spatiotemporally-resolved far-from-equilibrium dynamics during direct ink writing 3D printing. Here, Lithium Titanate (LTO) based ink is prepared and rheologically tested for its shear-thinning properties. Two-time intensity-intensity functions are calculated to be used in subsequent quantitative analysis, which allows for an overall characterization of the dynamics, description of an initial fast decorrelation and identification of sudden rearrangements of subdomains of the sample. The results show the dynamics to be anisotropic, spatiotemporally heterogenous and marked by distinct rearrangement events, all of which impact the electrochemical performance of energy storage devices. The studied 3D printing ink is used to fabricate electrodes which are then electrochemically tested, showing good performance in cycling and retaining structural integrity. This work furthers the understanding of the far-from-equilibrium material dynamics during 3D printing, giving quantitative characterization of this process, and highlights aspects of structure formation relevant to the electrochemical performance of the resultant energy storage device.
Vascular tone is dependent on smooth muscle K ATP channels comprising pore-forming Kir6.1 and regulatory SUR2B subunits, in which mutations cause Cantú syndrome. Unique among K ATP isoforms, they lack spontaneous activity and require Mg-nucleotides for activation. Structural mechanisms underlying these properties are unknown. Here, we determined cryogenic electron microscopy structures of vascular K ATP channels bound to inhibitory ATP and glibenclamide, which differ informatively from similarly determined pancreatic K ATP channel isoform (Kir6.2/SUR1). Unlike SUR1, SUR2B subunits adopt distinct rotational “propeller” and “quatrefoil” geometries surrounding their Kir6.1 core. The glutamate/aspartate-rich linker connecting the two halves of the SUR-ABC core is observed in a quatrefoil-like conformation. Molecular dynamics simulations reveal MgADP-dependent dynamic tripartite interactions between this linker, SUR2B, and Kir6.1. The structures captured implicate a progression of intermediate states between MgADP-free inactivated, and MgADP-bound activated conformations wherein the glutamate/aspartate-rich linker participates as mobile autoinhibitory domain, suggesting a conformational pathway toward K ATP channel activation.
Supported noble metal catalysts, ubiquitous in chemical technology, often undergo dynamic transformations between reduced and oxidized states—which influence the metal nuclearities, oxidation states, and catalytic properties.
The emission of white light from a single material is atypical and is of interest for solid-state lighting applications. Broadband light emission has been observed in some layered perovskite derivatives, A 2 PbBr 4 (A = R-NH 3 + ), and correlates with static structural distortions corresponding to out-of-plane tilting of the lead bromide octahedra. While materials with different organic cations can yield distinct out-of-plane tilts, the underlying origin of the octahedral tilting remains poorly understood. Using high energy resolution (e.g., quasi-elastic) neutron scattering, this contribution details the rotational dynamics of the organic cations in A 2 PbBr 4 materials where A = n-butylammonium (nBA), 1,8-diaminooctammonium (ODA), and 4-aminobutyric acid (GABA). The organic cation dynamics differentiate (nBA) 2 PbBr 4 from (ODA)PbBr 4 or (GABA) 2 PbBr 4 in that the larger spatial extent of dynamics of nBA yields a larger effective cation radius. The larger effective volume of the nBA cation in (nBA) 2 PbBr 4 yields a closer to ideal A-site geometry, preventing the out-of-plane tilt and broadband luminescence. In all three compounds, we observe hydrogen dynamics attributed to rotation of the ammonium headgroup and at a time scale faster than the white light photoluminescence studied by time-correlated single photon counting spectroscopy. This supports a previous assignment of the broadband emission as resulting from a single ensemble, such that the emissive excited state experiences many local structures faster than the emissive decay. Furthermore, the findings presented here highlight the role of the organic cation and its dynamics in hybrid organic–inorganic perovskites and white light emission.
This review spotlights the role of atomic-level modeling in research on metal-organic frameworks (MOFs), especially the key methodologies of density functional theory (DFT), Monte Carlo (MC) simulations, and molecular dynamics (MD) simulations. The discussion focuses on how periodic and cluster-based DFT calculations can provide novel insights into MOF properties, with a focus on predicting structural transformations, understanding thermodynamic properties and catalysis, and providing information or properties that are fed into classical simulations such as force field parameters or partial charges. Classical simulation methods, highlighting force field selection, databases of MOFs for high-throughput screening, and the synergistic nature of MC and MD simulations, are described. By predicting equilibrium thermodynamic and dynamic properties, these methods offer a wide perspective on MOF behavior and mechanisms. Additionally, the incorporation of machine learning (ML) techniques into quantum and classical simulations is discussed. These methods can enhance accuracy, expedite simulation setup, reduce computational costs, as well as predict key parameters, optimize geometries, and estimate MOF stability. By charting the growth and promise of computational research in the MOF field, the aim is to provide insights and recommendations to facilitate the incorporation of computational modeling more broadly into MOF research.
Oxide-supported noble metal catalysts have been extensively studied for decades for the water gas shift (WGS) reaction, a catalytic transformation central to a host of large volume processes that variously utilize or produce hydrogen. There remains considerable uncertainty as to how the specific features of the active metal-support interfacial bonding—perhaps most importantly the temporal dynamic changes occurring therein—serve to enable high activity and selectivity. Here we report the dynamic characteristics of a Pt/CeO 2 system at the atomic level for the WGS reaction and specifically reveal the synergistic effects of metal-support bonding at the perimeter region. We find that the perimeter Pt 0 -O vacancy -Ce 3+ sites are formed in the active structure, transformed at working temperatures and their appearance regulates the adsorbate behaviors. We find that the dynamic nature of this site is a key mechanistic step for the WGS reaction.
Significance The physical origin of cooperative activated relaxation in glass-forming liquids, which underlies the huge growth of viscosity and suppression of diffusion with cooling, remains elusive. Understanding this problem is of fundamental scientific interest and can assist in the design of new materials. We combine experimental relaxation time and equation-of-state data of molecular liquids to provide strong evidence for the recent theoretical prediction that activated relaxation, though causally driven by dynamically coupled cage-scale hopping and nonlocal collective elasticity quantified by local structural correlations, is well captured based on a thermodynamic description with dimensionless compressibility as the key variable. A mechanistic deduction is the crossover from fragile to strong (e.g., inorganic networks) relaxation behavior arises from the irrelevance of long-range elasticity effects.