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The unfolding dynamics of ubiquitin were studied using a combination of x-ray solution scattering (XSS) and molecular dynamics (MD) simulations. The kinetic analysis of the XSS ubiquitin signals showed that the protein unfolds through a two-state process, independent of the presence of destabilizing salts. In order to characterize the ensemble of unfolded states in atomic detail, the experimental XSS results were used as a constraint in the MD simulations through the incorporation of x-ray scattering derived potential to drive the folded ubiquitin structure toward sampling unfolded states consistent with the XSS signals. We detail how biased MD simulations provide insight into unfolded states that are otherwise difficult to resolve and underscore how experimental XSS data can be combined with MD to efficiently sample structures away from the native state. Our results indicate that ubiquitin samples unfolded in states with a high degree of loss in secondary structure yet without a collapse to a molten globule or fully solvated extended chain. Finally, we propose how using biased-MD can significantly decrease the computational time and resources required to sample experimentally relevant nonequilibrium states. [ABSTRACT FROM AUTHOR]

Here, a recently commissioned five‐analyzer Johann spectrometer at the Inner Shell Spectroscopy beamline (8‐ID) at the National Synchrotron Light Source II (NSLS‐II) is presented. Designed for hard X‐ray photon‐in/photon‐out spectroscopy, the spectrometer achieves a resolution in the 0.5–2 eV range, depending on the element and/or emission line, providing detailed insights into the local electronic and geometric structure of materials. It serves a diverse user community, including fields such as physical, chemical, biological, environmental and materials sciences. This article details the mechanical design, alignment procedures and data‐acquisition scheme of the spectrometer, with a particular focus on the continuous asynchronous data‐acquisition approach that significantly enhances experimental efficiency. [ABSTRACT FROM AUTHOR]

Autonomous methods to align beamlines can decrease the amount of time spent on diagnostics, and also uncover better global optima leading to better beam quality. The alignment of these beamlines is a high‐dimensional expensive‐to‐sample optimization problem involving the simultaneous treatment of many optical elements with correlated and nonlinear dynamics. Bayesian optimization is a strategy of efficient global optimization that has proved successful in similar regimes in a wide variety of beamline alignment applications, though it has typically been implemented for particular beamlines and optimization tasks. In this paper, we present a basic formulation of Bayesian inference and Gaussian process models as they relate to multi‐objective Bayesian optimization, as well as the practical challenges presented by beamline alignment. We show that the same general implementation of Bayesian optimization with special consideration for beamline alignment can quickly learn the dynamics of particular beamlines in an online fashion through hyperparameter fitting with no prior information. We present the implementation of a concise software framework for beamline alignment and test it on four different optimization problems for experiments on X‐ray beamlines at the National Synchrotron Light Source II and the Advanced Light Source, and an electron beam at the Accelerator Test Facility, along with benchmarking on a simulated digital twin. We discuss new applications of the framework, and the potential for a unified approach to beamline alignment at synchrotron facilities. [ABSTRACT FROM AUTHOR]

Molten salts play an important role in various energy-related applications such as high-temperature heat transfer fluids and reaction media. However, the extreme molten salt environment causes the degradation of materials, raising safety and sustainability challenges. A fundamental understanding of material-molten salt interfacial evolution is needed. This work studies the transformation of metallic Cr in molten 50/50 mol% KCl-MgCl2 via multi-modal in situ synchrotron X-ray nano-tomography, diffraction and spectroscopy combined with density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. Notably, in addition to the dissolution of Cr in the molten salt to form porous structures, a d-A15 Cr phase was found to gradually form as a result of the metal-salt interaction. This phase change of Cr is associated with a change in the coordination environment of Cr at the interface. DFT and AIMD simulations provide a basis for understanding the enhanced stability of d-A15 Cr vs. bcc Cr, by revealing their competitive phase thermodynamics at elevated temperatures and probing the interfacial behavior of the molten salt at relevant facets. This study provides critical insights into the morphological and chemical evolution of metal-molten salt interfaces. The combination of multimodal synchrotron analysis and atomic simulation also offers an opportunity to explore a broader range of systems critical to energy applications. [ABSTRACT FROM AUTHOR]

The protein folding process often proceeds through partially folded transient states. Therefore, a structural understanding of these disordered states is crucial for developing mechanistic models of the folding process. Characterization of unfolded states remains challenging due to their disordered nature, and incorporating multiple methods is necessary. Combining the time-resolved x-ray solution scattering (TRXSS) signal with molecular dynamics (MD), we are able to characterize transient partially folded states of bovine α-lactalbumin, a model system widely used for investigation of molten globule states, during its unfolding triggered by a temperature jump. We track the unfolding process between 20 µs and 70 ms and demonstrate that it passes through three distinct kinetic states. The scattering signals associated with these transient species are then analyzed with TRXSS constrained MD simulations to produce protein structures that are compatible with the input signals. Without utilizing any experimentally extracted kinetic information, the constrained MD simulation successfully drove the protein to an intermediate molten globule state; signals for two later disordered states are refined to terminal unfolded states. From our examination of the structural characteristics of these disordered states, we discuss the implications disordered states have on the folding process, especially on the folding pathway. Finally, we discuss the potential applications and limitations of this method. [ABSTRACT FROM AUTHOR]

In the past few decades, prediction of macromolecular structures beyond the native conformation has been aided by the development of molecular dynamics (MD) protocols aimed at exploration of the energetic landscape of proteins. Yet, the computed structures do not always agree with experimental observables, calling for further development of the MD strategies to bring the computations and experiments closer together. Here, we report a scalable, efficient MD simulation approach that incorporates an x-ray solution scattering signal as a driving force for the conformational search of stable structural configurations outside of the native basin. We further demonstrate the importance of inclusion of the hydration layer effect for a precise description of the processes involving large changes in the solvent exposed area, such as unfolding. Utilization of the graphics processing unit allows for an efficient all-atom calculation of scattering patterns on-the-fly, even for large biomolecules, resulting in a speed-up of the calculation of the associated driving force. The utility of the methodology is demonstrated on two model protein systems, the structural transition of lysine-, arginine-, ornithine-binding protein and the folding of deca-alanine. We discuss how the present approach will aid in the interpretation of dynamical scattering experiments on protein folding and association. [ABSTRACT FROM AUTHOR]

In this work, we present a detailed investigation on the recombination dynamics of mercury halides HgX2 (X = I, Br) in acetonitrile solution after UV-induced photodissociation. The study is performed by combining time-resolved wide-angle x-ray scattering (TRWAXS) and optical transient absorption spectroscopy. Up to 68% of the UV (266 nm) photodissociated HgX and X radicals that escape the solvent cage surrounding parent HgX2 recombine within a nanosecond after photodissociation. In contrast to classical primary geminate recombination, occurring on much faster time scales, we interpret the sub-nanosecond recombination channel as secondary geminate recombination (SGR), also referred to as diffusion-limited geminate recombination. The family of triatomic mercury halides therefore represents an important class of molecules to study chemical mechanisms of solvent-dependent SGR by TRWAXS. The methodology described here allows for direct mapping of the time-dependent inter-radical distance distribution function, a critical parameter for the assessment of the SGR dynamics in solution phase and solvation in general. [ABSTRACT FROM AUTHOR]

Mixed-valence cerium oxide nanoparticles (nanoceria) have been investigated with pronounced interest due to a wide range of biomedical and industrial applications that arises from its remarkable redox catalytic properties. However, there is no understanding of how to control the formation of these two types of nanoceria to obtain Ce3+/Ce4+ ratios required in various applications. In this work, using a soluble borate glass, nanoceria with specific ratios of Ce3+/Ce4+ are created and extracted via controlled glass-melting parameters. Glass embedded with nanoceria as well as nanoceria extracted from the glass were studied via XANES and fitted with the Multivariate Curve Resolution (MCR) technique to calculate the ratio of Ce3+/Ce4+. Results show that mixed-valence nanoceria with specific ratios are hermetically sealed within the glass for long durations. When the glass dissolves, the mixed-valence nanoceria are released, and the extracted nanoceria have unchanged Ce3+/Ce4+ ratios. Furthermore, TEM investigation on released nanoceria show that the nanoceria consist of several different structures. Although nanocrystal structures of Ce7O12, Ce11O20, and Ce2O3 contribute to the reduced state, a new quasi-stable phase of CeO1.66 has been observed as well. [ABSTRACT FROM AUTHOR]

In this study, we demonstrate three-dimensional (3D) hollow nanosphere electrocatalysts for CO2 conversion into formate with excellent H-Cell performance and industrially-relevant current density in a 25 cm2 membrane electrode assembly electrolyzer device. Varying calcination temperature maximized formate production via optimizing the crystallinity and particle size of the constituent SnO2 nanoparticles. The best performing SnO2 nanosphere catalysts contained ~ 7.5 nm nanocrystals and produced 71–81% formate Faradaic efficiency (FE) between −0.9 V and −1.3 V vs. the reversible hydrogen electrode (RHE) at a maximum formate partial current density of 73 ± 2 mA cmgeo−2 at −1.3 V vs. RHE. The higher performance of nanosphere catalysts over SnO2 nanoparticles and commercially-available catalyst could be ascribed to their initial structure providing higher electrochemical surface area and preventing extensive nanocrystal growth during CO2 reduction. Our results are among the highest performance reported for SnO2 electrocatalysts in aqueous H-cells. We observed an average 68 ± 8% FE over 35 h of operation with multiple on/off cycles. In situ Raman and time-dependent X-ray diffraction measurements identified metallic Sn as electrocatalytic active sites during long-term operation. Further evaluation in a 25 cm2 electrolyzer cell demonstrated impressive performance with a sustained current density of 500 mA cmgeo−2 and an average 75 ± 6% formate FE over 24 h of operation. Our results provide additional design concepts for boosting the performance of formate-producing catalysts. [ABSTRACT FROM AUTHOR]

Two-dimensional transition metal trichalcogenides (TMTCs) feature covalently bonded metal-chalcogen layers separated by the van der Waals (vdW) gap. Similar to transition metal dichalcogenides (TMDCs), TMTCs often host charge density waves (CDWs) and superconductivity, but unlike TMDCs, atomic chains in the crystal structure give rise to quasi one-dimensional (quasi 1D) conduction. ZrTe3 features the CDW below T CDW = 63 K and filamentary superconductivity below 2 K that can be enhanced by pressure or chemical substitution. Here, we report the presence of mixed valent Zr2+ and Zr4+ atoms in ZrTe3 crystals that are reduced by doping in ZrTe3−xSex and Zr1−yHfyTe3. Superconductivity is enhanced via disorder in Te2-Te3 atomic chains that are associated with CDW formation. Hf substitution on the Zr atomic site enhances T CDW due to unperturbed Te2-Te3 chain periodicity and enhanced electron-phonon coupling. Weak electronic correlations in ZrTe3−xSex are likely governed by the lattice contraction effects. [ABSTRACT FROM AUTHOR]