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At least 19 records

Structure refinement and anisotropic atomic displacement parameters of 1M Illite: Rietveld and pair distribution function analysis using synchrotron X-ray radiation

Illite, a widespread clay mineral, plays a pivotal role in geological processes, notably as an indicator in diagenetic and hydrothermal alteration environments, and possesses significant industrial relevance in applications including ceramics, construction and catalysis. However, challenges including its nanoscale crystallinity, structural disorder and frequent interstratification with other clay minerals have hindered detailed structural characterization using conventional X-ray diffraction (XRD) techniques. This study employs integrated synchrotron XRD and pair distribution function (PDF) analysis to elucidate the crystal structure of the 1M illite polytype, yielding the first determination of its anisotropic atomic displacement parameters (U aniso ). TheseU aniso parameters provide critical insights into atomic dynamics and static disorder within the structure, enabling a more refined understanding of structure–property relationships. This integrated approach, combining synchrotron XRD, Rietveld refinement and PDF analysis, yields a comprehensive structural characterization, capturing both average crystallographic and local atomic arrangements. Considering illite's widespread geological occurrence and industrial importance, this high-precision structural dataset, especially the determinedU aniso values, provides a crucial benchmark for future modeling and simulation efforts targeting accurate prediction of its physicochemical behavior.

Chemistry

AUTOIGNITION DELAY TIMES FOR REFORMATE GAS MIXTURES FROM METHANE GAS ENGINES

Methane slip is a prominent issue in natural gas reciprocating engines that are used in transportation and marine applications. The incomplete combustion that results in methane slip can be resolved with the introduction of hydrogen within the combustion mixture to improve methane oxidation and further enable combustion within the engine crevices where methane has previously remained unreacted. Steam methane reforming (SMR) is a common method used to produce hydrogen and can be used to design an onboard device to reduce methane slip from reciprocating engines. The development of this reformer device requires the validation of high-fidelity chemical kinetic models at the low temperatures of the crevice volumes of these engines. In this work, auto-ignition data is obtained using a shock tube at lean (φ—0.714 or λ—1.4) and stoichiometric (φ, λ = 1) equivalence ratios spanning a temperature range of 1042–1234 K at the 80-bar operating pressure of the test engine. Blends of methane, hydrogen, and reformate products from the SMR reaction are shock-heated in synthetic air, with the ignition delay time measured using an OH* chemiluminescence detector at 310 nm and a CH* detector at 430 nm. The experimental results are compared to several state-of-the-art chemical kinetic mechanisms from the literature. In general, most of the mechanisms show very good agreement with experiments at higher temperatures, with simulation results showing little deviation from experiments at lower temperatures. A sensitivity analysis was conducted, and the results reveal that the reaction H2 + CH3O2 = H + CH3O2H has a very significant role in determining low-temperature ignition delay times (IDTs) of SMR mixtures. These findings provide valuable insights into the chemical kinetics governing methane reformate combustion and contribute to the optimization of onboard reformer designs aimed at mitigating methane slip in natural gas-fueled engines.

Fraze, Matthew

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields

In macromolecular structure refinement, the low observation-to-parameter ratio and the lack of high-resolution data are countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate chemical restraints and, therefore, accurate macromolecular structures. In particular, it is desirable to have accurate restraints for known and novel ligand entities. Quantum mechanics (QM) can minimize the energy of a ligand by adjusting its geometry, and these geometries can be used to generate restraints for macromolecular refinement. This article describes a library of approximately 37 000 small molecules extracted from the Chemical Component Dictionary in the Protein Data Bank and minimized by density-functional QM. The library includes restraint files for use in crystallography or cryo-EM refinement, along with files suitable for molecular-dynamics simulation. Because the geometries are validated using the Cambridge Structural Database, the restraints library provides users with both functional restraints and minimized geometries. This work also provides procedures for generating new and accurate restraints.

Amber

Higher Dimensionality in the Mg–Co–B System: Synthesis and Structure of Incommensurate Composite Mg 1+ε Co 4 B 4

Guided by high-temperature in situ X-ray diffraction, the discovery and synthesis of Mg 1+ε Co 4 B 4 (ε ≈ 0.272) using a MgH 2 hydride precursor is reported, along with a detailed crystal structure description and measurement of magnetic properties. The mismatch in lattice periodicities between Mg and Co–B substructures places Mg 1+ε Co 4 B 4 in the family of incommensurate composite crystals and prompted structural refinement in a (3 + 1)-dimensional model. The structure of Mg 1+ε Co 4 B 4 (P4 2 /ncm(00γ)s00s, a = 6.75847(7) Å, c = 3.94007(8) Å, q = (0, 0, 1.2721(3))) was refined from neutron powder diffraction and high-resolution powder X-ray diffraction data and confirmed by scanning transmission electron microscopy and electron diffraction. Mg 1+ε Co 4 B 4 is isostructural to Nd 1+ε Fe 4 B 4 and several related ternary borides with 0.07 ≤ ε ≤ 0.17, with Mg occupying the rare-earth site. Satellite reflections in the electron diffraction patterns hinted at positional modulation of the transition metal–boron substructure by Mg atoms, but this could not be refined from the neutron or X-ray diffraction data. Low-temperature magnetic measurements show no indications of long-range magnetic ordering or superconductivity down to 5 K. DFT calculations confirmed the absence of a magnetically ordered ground state and the stability of a 5:4 supercell (ε = 0.25) relative to the fully commensurate structure. Neutron diffraction and synthesis from elemental Mg demonstrated that Mg 1+ε Co 4 B 4 is not a hydrogen-stabilized phase. Mg 1+ε Co 4 B 4 represents the second compound reported in the Mg–Co–B system and the first superspace symmetry model of a Nd 1+ε Fe 4 B 4 -type incommensurate composite compound refined from powder diffraction data.

chemical structure

The Alamo multiphysics solver for phase field simulations with strong-form mechanics and block structured adaptive mesh refinement

Alamo is a high-performance scientific code that uses block-structured adaptive mesh refinement to solve such problems as: the ignition and burn of solid rocket propellant, plasticity, damage and fracture in materials undergoing loading, and the interaction of compressible flow with eroding solid materials. Alamo is powered by AMReX, and provides a set of unique methods, models, and algorithms that enable it to solve solid-mechanics problems (coupled to other physical behavior such as fluid flow or thermal diffusion) using the power of block-structured adaptive mesh refinement.

36 MATERIALS SCIENCE

MXene-Derived Potassium-Preintercalated Bilayered Vanadium Oxide Nanostructures for Cathodes in Nonaqueous K-Ion Batteries

Bilayered vanadium oxides (BVOs) are promising cathode materials for beyond-Li-ion batteries due to their tunable chemistries and high theoretical capacities. However, the large size of beyond-Li + ions limits electrochemical cycling and rate capability of BVO electrodes. Recent reports of MXene-derived BVOs with nanoscale flower-like morphology have shown improved electrochemical stability at high rates up to 5C in nonaqueous lithium-ion batteries. Here, we report how morphological stabilization can lead to improved rate capability in potassium-ion batteries (PIBs) through the synthesis and electrochemical characterization of MXene-derived K-preintercalated BVOs (MD-KVOs), which were derived from two V 2 CT x precursor materials prepared using two different etching protocols. We show that the etching conditions affect the surface chemistry of the MXene, which plays a role in the MXene-to-oxide transformation process. MXene derived from a milder etchant transformed into a nanoflower MD-KVO with two-dimensional (2D) nanosheet petals (KVO-DMAE) while a more aggressive etchant produced a MXene that transformed into a MD-KVO with one-dimensional (1D) nanorod morphology (KVO-CMAE). Electrochemical cycling of the produced MD-KVOs after drying at 200 °C under vacuum (KVO-DMAE-200 and KVO-CMAE-200) in PIBs showed that electrochemical stability of MD-KVO at high rates improved through the morphological stabilization of 2D particles combined with the control of interlayer water and K + ion content. Structure refinement of KVO-DMAE-200 further corroborates the behavior observed during K + ion cycling, connecting structural and compositional characteristics to the improved rate capability. This work demonstrates how proper synthetic methodology can cause downstream effects in the control of structure, chemical composition, and morphology of nanostructured layered oxide materials, which is necessary for development of future materials for beyond-Li-ion battery technologies.

25 ENERGY STORAGE

Bridging Experiment and Theory to Reveal Compounds in K–Zn(Cd)–Bi Systems

This study investigates the facile hydride synthesis method guided by theoretical predictions to explore the K–T–Bi (T = Zn, Cd) phase spaces. Using an adaptive genetic algorithm (AGA) and density functional theory (DFT), candidate compositions are identified for experimental validation via a facile hydrides route, permitting experimental screening of K–Zn–Bi and “empty” K–Cd–Bi systems. The previously reported KZnBi and KZn 2 Bi 2 are synthesized alongside newly discovered KCdBi and KCd 2 Bi 2 . While the AGA and DFT predict the stability of these compounds, structural predictions align with the experiment only for KZnBi and KZn 2 Bi 2 . Single-crystal X-ray structure refinements confirm that KZnBi and KZn 2 Bi 2 adopt the hexagonal ZrBeSi- and tetragonal ThCr 2 Si 2 -structure types, respectively. KCdBi has tetragonal PbClF-structure type and KCd 2 Bi 2 belongs to the ThCr 2 Si 2 -structure type. A trend based on the ratio of the metal ionic radii allows to rationalize variation in the structure types within the ATBi family (A = Li–Cs), correctly identifying KCdBi as isostructural to NaZnBi. Thermal stability studied by high-temperature powder X-ray diffraction reveals that Zn-containing compounds melt at higher temperatures (821 K for KZn 2 Bi 2 ) than Cd-containing KCd 2 Bi 2 (635 K). This study highlights the efficacy of combining rapid synthesis techniques with predictive modeling, though structural predictions show some limitations in accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Dynamics and Structure of Molten Neodymium Titanate

Binary rare earth titanates can be vitrified using levitation melt quenching, and their glasses are promising for optical applications. To better understand their thermophysical properties and dynamics, we have used molecular dynamics (MD) and empirical potential structure refinement (EPSR) to simulate molten neodymium titanate, 83TiO 2 –17Nd 2 O 3 . The models are compared with high-energy synchrotron X-ray diffraction of the melt structure over 1060–1960 K and thermophysical property measurements of electrostatically levitated droplets over 1500–2200 K. As temperature increases, the network periodicity increases and the correlation length decreases, both in monotonic trends that suggest continuous structural evolution through the melt and supercooled liquid regimes. At 1900 K, the mean Ti–O and Nd–O coordination numbers are 5.8(5) and 6.7(5), compared to the glass, 5.72(6) and 7.70(26). The equilibrium melting point is measured as 1860(20) K, over 100 K higher than previous estimates. Viscosity data from MD are in good agreement with experimental measurements. The dynamic propensity of Nd is similar to that of the network-forming Ti, suggesting that Nd does not participate as a conventional modifier. The viscosity of this fragile liquid is likely controlled by the breaking of cation–oxygen bonds and rearrangements of Ti–O polyhedra.

molecular dynamics

Structure of molten ytterbium aluminum garnet

Rare earth aluminum garnets are important materials in optical, dielectric, and thermal barrier applications. To advance the understanding of their melt processing and glass forming ability, we report the atomic structure of molten Yb 3 Al 5 O 12 over 1770–2630 K, which spans the equilibrium and supercooled liquid regimes. The melt density at T m = 2283 K is 5.50 g cm –3 , measured via silhouette imaging of electrostatically levitated drops over 1010–2420 K. Four separate structure measurements were made with aerodynamically levitated melts using x-ray and neutron diffraction with isotope substitution of Yb ( 172 Yb, 174 Yb, or nat Yb). Empirical potential structure refinement models were developed, which are in excellent agreement with the experiments. Coordination environments for Al–O are predominantly 4- and 5-coordinate, with a mean coordination of n AlO = 4.43(8), while Yb–O environments mostly range from 5- to 8-coordinate, with n YbO = 6.26(8). The cation–oxygen polyhedra are connected primarily by corner-sharing, with edge-sharing constituting up to ~1/3 of the connectivity among polyhedra with Yb or higher-coordinated Al–O. Structurally, the –Al–O– network in molten Yb 3 Al 5 O 12 appears conducive to glass formation: n OAl = 1.85(3), there are 1.86 AlO x –AlO x connections per Al atom (e.g., a mixture of Q 3 and Q 4 units), and the modal ring size is six cations. These characterize a network that is somewhat less constrained compared to SiO 2 glass, yet Yb 3 Al 5 O 12 cannot be quenched into crystal-free glass. Here, aluminum garnet compositions with larger rare earth cations do form glass, so these characterizations help reveal the structural characteristics corresponding to the limit of glass forming ability in rare earth aluminates.

36 MATERIALS SCIENCE

Local structure of zinc–indium–tin oxide films via grazing-incidence x-ray pair-distribution functions and theoretical methods

A detailed experimental and theoretical study on the local (r ≤ 4.5 Å) atomic structure of amorphous and crystalline zinc–indium–tin oxide (ZITO) thin films using grazing-incidence x-ray Pair-Distribution Functions (PDFs), ab initio Molecular Dynamics (MD), and Empirical Potential Structure Refinement (EPSR) Monte Carlo simulations is presented. High-energy synchrotron x rays, a two-dimensional detector, and different incident angles were used to probe the depth uniformity of five (ZnO) 0.15 (In 2 O 3 ) 0.70 (SnO 2 ) 0.15 films that were deposited via pulsed-laser deposition at growth temperatures (T G ) ranging from 25 to 300 °C. Films deposited at T G ≤ 150 °C were amorphous. The partially crystalline (T G = 200 °C) and fully crystalline (T G = 300 °C) films were highly textured. Both crystalline and amorphous structures were investigated using ab initio MD and EPSR Monte Carlo simulations. The density of the amorphous films determined from the experimental data agreed with MD calculations. Coordination numbers, bond lengths, and distortion for metal–oxygen and for both the edge- and corner-shared In–metal shells up to 4.5 Å obtained from PDF analysis closely agreed with MD and EPSR simulations. There is a pronounced decrease in the edge- and corner-shared In–Zn distances arising from the shorter Zn–O bond length, Zn–O tetrahedral coordination, and In–O–Zn angle in amorphous ZITO compared to its crystalline counterpart. A maximum in electrical mobility was observed for the amorphous film just before crystallization occurred. While the peak is broad, consistent with nearly unchanged overall cation–oxygen coordination in the amorphous films, ESPR results indicate that the tetrahedral coordination follows the conductivity trend.

Grazing Incidence X-ray

Structure and ultrafast dynamics of tri-nuclear Ag-/Tl–Pt 2 POP 4 complexes in solution

The energetics and dynamics of ion assembly in solution has broad influence in nanomaterials and inorganic synthesis. To investigate the fundamental processes involved, we present a time-resolved x-ray solution scattering (TR-XSS) study of the trinuclear silver and thallium complexes of the diplatinum ion PtPOP [Pt 2 (H 2 P 2 O 5 )$_4^{4−}$] in aqueous solution. These complexes, their structural properties, and their electronic structure are not well understood and afford a unique opportunity to study the metal–metal bond formation that influences molecular and material assembly in solution. We present model-independent analysis of the observed dynamics as well as an analysis incorporating time-resolved structural refinements of key bond lengths with $<$100 fs time resolution. We find that upon photoexcitation, the Pt atoms contract ∼0.25 Å toward the center of both the Ag- and the Tl-PtPOP complexes, as previously observed for the PtPOP anion. For the AgPtPOP system, an ultrafast Ag-Pt bond expansion of ∼0.2 Å is observed, whereas in contrast, the TlPtPOP system exhibits a Tl-Pt bond contraction of ∼0.3 Å upon photoexcitation. For both complexes, the change in electronic state leads to coherent (“wave-packet”) oscillations along the metal–Pt coordinates. Based on these structural dynamics, we propose an electronic structure model that describes the metal–metal bonding behavior in both the ground and excited state for both complexes.

Lenzen, Philipp [Technical Univ. of Denmark, Lyngb

The Molecular Structures of Liquid and Glassy Nifedipine and Felodipine and Their Incorporation into PVP

Background: Amorphous drug formulations are commonly used to improve the solubility and bioavailability of poorly soluble molecular pharmaceuticals, yet less is known about their molecular conformations and local bonding interactions than their crystalline phases. Methods: High-energy X-ray diffraction structure factor measurements have been made on liquid and glassy nifedipine (NIF), felodipine (FEL), NIF 1:3 polyvinylpyrrolidone (PVP), and FEL 1:3 PVP wt.% mixtures. The corresponding X-ray pair distribution functions have been interpreted using empirical potential structure refinement using different models and density functional theory conformer calculations. Results: In both NIF and FEL, the NH···O inter-molecular hydrogen bonds between the pyridyl nitrogen and ester carbonyls are found to be considerably weaker than those observed in the crystalline polymorphs. For nifedipine, it is proposed that either inter-molecular NH…ON nitro bonds are present and/or a fraction (<20%) of conformational changes, with the aryl ring flipped, occur in the liquid state. For felodipine, the models indicate significant disorder associated with the methyl and ethyl side chains in the liquid state, with the main peak intensity at 3.0 Å arising from intra-molecular Cl-Cl atom pairs. When nifedipine molecules are incorporated into PVP, our models show they possess stronger NH···O bonds to the PVP polymer than felodipine molecules, which have stronger affinity for bonding to the polymer than to other felodipine molecules. Conclusions: The amorphous forms of both NIF and FEL show much weaker hydrogen bonding than found in their crystalline phases. Liquid NIF also exhibits configurations which are not observed in the crystal phases.

Amorphous Solid Dispersion

Emergent topological polarization textures in relaxor ferroelectrics

Relaxor ferroelectrics underpin high-performance actuators and sensors, yet the nature of polar heterogeneities driving their broadband dielectric response remains debated. Using a unified, multimodal structural refinement framework— simultaneously fitting complementary X-ray and neutron total scattering, X-ray absorption spectra, and diffuse scattering—we reconstruct 3D mesoscale polarization maps in the classic relaxor system PbMg 1/3 Nb 2/3 O 3 –PbTiO 3 . We uncover self-organized swirling polarization textures with half-skyrmion (meron) vortices, challenging models of independent polar nanoregions. These textures, characterized by smooth changes in the polarization direction, originate from overlapping volumes in which the projections of locally correlated polarization vectors onto each volume’s long axis share the same sign. Vortex cores correlate strongly with local charge and strain gradients imposed by compositional heterogeneities. In this work, our results suggest that chemical disorder, acting via depolarizing and strain fields, stabilizes topological vortex textures of the polarization field, offering a route for engineering new dielectric and ferroelectric functionalities.

Eremenko, Maksim [National Institute of Standards

On symmetry-resolved generalized entropies

Symmetry-resolved entanglement, capturing the refined structure of quantum entanglement in systems with global symmetries, has attracted a lot of attention recently. In this manuscript, introducing the notion of symmetry-resolved generalized entropies, we aim to develop a computational framework suitable for the study of excited state symmetry-resolved entanglement as well as the dynamical evolution of symmetry-resolved entanglement in symmetry-preserving out-of-equilibrium settings. We illustrate our framework using the example of (1+1)-d free massless compact boson theory, and benchmark our results using lattice computation in the XX chain. As a byproduct, our computational framework also provides access to the probability distribution of the symmetry charge contained within a subsystem and the corresponding full counting statistics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

Core Model Proposal #410: Updates to Socioeconomic and Macroeconomic Data, Processing Structure, and Visualization

This Core Model Proposal (CMP) comprehensively restructures and updates the macroeconomic and socioeconomic modules in gcamdata. It includes visualizations of key data inputs, accounting identities, and data flows in the context of GCAM-Macro-KLEM. Major improvements include: (1) updating the Penn World Table (PWT) to version 10 and incorporating a new source, the Global Macro Database (GMD); (2) updating the SSP socioeconomics database from version 3.0.1 to 3.2; (3) introducing SSP-specific differentiation of employment and labor force data; (4) improving data integration between national accounts (from PWT, GMD, and GTAP) and GDP/population data from external sources; and (5) general data cleaning and structural refinements. We document the data sources and key assumptions used throughout the processing. These updates establish the foundation for the forthcoming KLEAM version of GCAM-macro.

97 MATHEMATICS AND COMPUTING

AQuaRef: machine learning accelerated quantum refinement of protein structures

Cryo-EM and X-ray crystallography provide crucial experimental data for obtaining atomic-detail models of biomacromolecules. Refining these models relies on library-based stereochemical data, which, in addition to being limited to known chemical entities, do not include meaningful noncovalent interactions. Quantum mechanical (QM) calculations could alleviate these issues but are too expensive for large molecules. Here we present a novel AI-enabled Quantum Refinement (AQuaRef) based on AIMNet2 machine learned interatomic potential (MLIP) mimicking QM at substantially lower computational costs. By refining 41 cryo-EM and 30 X-ray structures, we show that this approach yields atomic models with superior geometric quality compared to standard techniques, while maintaining an equal or better fit to experimental data. Notably, AQuaRef aids in determining proton positions, as illustrated in the challenging case of short hydrogen bonds in the parkinsonism-associated human protein DJ-1 and its bacterial homolog YajL.

Zubatyuk, Roman [Carnegie Mellon University, Pitts

Structure of ice VII with Hirshfeld atom refinement

In the refinement of the crystal structures of ice, the best results obtained so far have been with neutron diffraction because the most troublemaking aspects are the hydrogen atoms. In nine out of twenty ice structures, the hydrogen atoms are disordered, which makes proper refinement more difficult. In our previous paper describing the structure of ice VI we proved that, using Hirshfeld atom refinement (HAR) based on synchrotron X-ray data, it is possible to obtain results comparable with those from neutron experiments. In this work, we investigate another structure of high-pressure disordered ice, cubo-ice (ice VII). Single crystals of cubo-ice were grown under pressure in diamond anvil cells. X-ray diffraction measurements were conducted at a synchrotron source facility (APS, University of Chicago, USA) as well as on our regular in-house laboratory diffractometer with Ag radiation. The data collected were further refined with HAR. Comparison of the structural parameters obtained with those derived from neutron diffraction showed very good agreement in terms of bond lengths and fairly good agreement in terms of hydrogen atom ADPs. We were also able to perform unconstrained refinements with various split-atom models.

Chemistry