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At least 73 records · Page 4

Grain incompatibility determines the local structure of amorphous grain boundary complexions

Amorphous grain boundary complexions lack long-range crystalline order but are not featureless, as distinct gradients in structural short-range order have been reported through their thickness. In this work, we test the hypothesis that the distribution of short-range order is determined by the confining crystals using atomistic simulations of both Cu-Zr bicrystals and a random polycrystal. Voronoi polyhedra with structures similar to that of perfect face-centered cubic serve as signatures of high structural order and are only found at the amorphous-crystalline transition regions. The density of the ordered structural motifs within a specific amorphous-crystalline transition region is found to not be directly determined by the orientation and symmetry of the grain which touches it, but rather by the incompatibility between the two confining grains. Further, ordered polyhedra density is found to be inversely related to grain incompatibility, meaning that large incompatibilities between the confining crystals lead to less order in the amorphous-crystalline transition region. The finding that the entire grain-film-grain system must be considered to understand local structure unequivocally demonstrates that amorphous complexions are not simply a collection of independent phases which happen to nucleate at a grain boundary. Rather, an amorphous grain boundary complexion is a single entity that finds a local equilibrium configuration.

36 MATERIALS SCIENCE↗

Atomic-Layer-Deposited Aluminum Oxide Thin Films Probed with X-ray Scattering and Compared to Molecular Dynamics and Density Functional Theory Models

A better understanding of amorphous aluminum oxide’s structure and electronic properties is obtained through combined experimental and computational approaches. Grazing incidence X-ray scattering measurements were carried out on aluminum oxide thin films grown using thermal atomic layer deposition. The corresponding pair distribution functions (PDFs) showed structures similar to previously reported PDFs of solid-state amorphous alumina and molten alumina. Structural models based on crystalline alumina polymorphs (PDFgui) and amorphous alumina (molecular dynamics, MD) were examined for structural comparisons to the experimental PDF data. Smaller MD models were optimized and verified against larger models to allow for quantum chemical electronic structure calculations. The electronic structure of the amorphous alumina models yields additional insight into the band structure and electronic defects present in amorphous alumina that are not present in crystalline samples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Apex hydrogen bonds in dendron assemblies modulate close-packed mesocrystal structures

The close-packed mesocrystal structures from soft-matter assemblies have recently received attention due to their structural similarity to atomic crystals, displaying various sphere-packing Frank–Kasper (FK) and quasicrystal structures. Herein, diverse mesocrystal structures are explored in second-generation dendrons (G2-X) designed with identical wedges, in which the terminal functionalities X = CONH 2 and CH 2 NH 2 represent two levels of the strong and weak hydrogen-bonding apexes, respectively. The cohesive interactions at the core apex, referred to as the core interactions, are effectively modulated by forming heterogeneous hydrogen bonds between these two functional units. For the dendron assemblies compositionally close to each pure component of G2-CONH 2 and G2-CH 2 NH 2 , their own FK A15 and C14 phases dominate other phases, respectively. We show the existence of the wide-range FK σ including the dodecagonal quasicrystal (DDQC) phases from the dendron mixtures between G2-CONH 2 and G2-CH 2 NH 2 , providing an experimental phase sequence of A15–σ–DDQC–C14 as the core interactions are alleviated. Intriguingly, the temperature dependence of particle sizes shows that the high plateau values of particle sizes are maintained equivalently until each threshold temperature (T th ), followed by a prompt decrease above the T th . A decrease in T th by alleviating the core interactions and its composition dependence suggest that the more size-dispersed particles, the more susceptibility to chain exchange with increasing temperature. Here our results on the formation of supramolecular dendron assemblies provide a guide to understand the core-interaction-dependent mesocrystal structures toward the fundamental principle underlying the temperature dependence of their particle sizes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparing CRT and Pandora Tagged Tracks in ICARUS

The ICARUS Liquid Argon Time Projection Chamber (LArTPC) is used to investigate short-baseline neutrino oscillations and the possible existence of sterile neutrinos. To aid in identifying and rejecting cosmic ray backgrounds, the system is outfitted with external Cosmic Ray Taggers (CRTs). The CRT is able to measure more tracks and at a wider range of angles, useful in further detailing future calibrations. This project compared the most probable values (MPVs) of charge deposition between CRT tagged and TPC tagged tracks. The Y-Z maps of charge scale for both datasets show a strong correlation, not just in their overall structure, but also in how they reflect known detector effects. Both reconstruction paths showed similar structures in their charge distribution, such as less effective wire section or mechanical support, confirming that CRT-tagged tracks, despite being external, respond to the same calibration landscape as Pandora tracks, validating previous Pandora reconstructions and values. Overall, the analysis supports the idea that the CRT tags are a useful addition to ICARUS calibration efforts. Their broad angular range and independence from Pandora reconstruction make them a helpful secondary tool and a potential asset in extending calibration across the detector volume.

Thayer, Abigail [Colorado State U.] (ORCID:0009000↗

Comparing CRT and Pandora Tagged Tracks in ICARUS

The ICARUS Liquid Argon Time Projection Chamber (LArTPC) is used to investigate short-baseline neutrino oscillations and the possible existence of sterile neutrinos. To aid in identifying and rejecting cosmic ray backgrounds, the system is outfitted with external Cosmic Ray Taggers (CRTs). The CRT is able to measure more tracks and at a wider range of angles, useful in further detailing future calibrations. This project compared the most probable values (MPVs) of charge deposition between CRT tagged and TPC tagged tracks. The Y-Z maps of charge scale for both datasets show a strong correlation, not just in their overall structure, but also in how they reflect known detector effects. Both reconstruction paths showed similar structures in their charge distribution, such as less effective wire section or mechanical support, confirming that CRT-tagged tracks, despite being external, respond to the same calibration landscape as Pandora tracks, validating previous Pandora reconstructions and values. Overall, the analysis supports the idea that the CRT tags are a useful addition to ICARUS calibration efforts. Their broad angular range and independence from Pandora reconstruction make them a helpful secondary tool and a potential asset in extending calibration across the detector volume.

Thayer, Abbie [Fermilab; Colorado State U.]↗

Tailoring the Gating Effect of Organic Cage via a Porous Liquid Approach

Porous liquids (PLs) represent a new frontier in material design combining the merits of solid porous host and liquid phase in gas separation and catalysis. Herein, the PL construction approach is harnessed to tailor the gating effect of organic cages toward enhanced gas separation. A type-II fluorinated PL (F-PL) is developed via liquifying a fluorinated organic cage (F-cage) by a fluorinated ionic liquid (F-IL). The F-cage is featured by a small window size (≈5.1 Å), high surface area, good stability under highly ionic conditions, and abundant fluorine moieties. The F-IL possesses high steric hindrance (bulky cation) and structure similarity with the F-cage (fluorinated alkyl chain in the anion). The existing status structure integrity of F-cage in F-IL upon F-PL formation is illustrated via spectroscopy and X-ray-based techniques. The existence of rigid voids in F-PL is illustrated by positron annihilation lifetime spectroscopy (PALS) and the improved gas uptake capacity than F-IL via pressure-swing CO 2 uptake isotherms (0–40) bar. Further, the comparison of the gas uptake behavior (CO 2 , N 2 , CH 4 , and Xe) of F-PL and F-cage, combining the computational simulation, highlights that the PL construction can be leveraged to tune the window size of porous scaffolds, leading to enhanced gas selectivity.

36 MATERIALS SCIENCE↗

Pausing ultrafast melting by timed multiple femtosecond-laser pulses

An intense femtosecond-laser excitation of a solid induces highly nonthermal conditions. In materials like silicon, laser-induced bond-softening leads to a highly incoherent ionic motion and eventually nonthermal melting. But is this outcome an inevitable consequence, or can it be controlled? Here, we performed ab initio molecular dynamics simulations of crystalline silicon after timed multiple femtosecond-laser pulse excitations with fluence above the nonthermal melting threshold. Our results demonstrate an excitation mechanism that pauses nonthermal melting and creates a metastable state instead, with an electronic structure similar to the ground state. This mechanism can be generalized to other materials, potentially enabling structural and/or electronic transitions to metastable phases in the high-excitation regime. In addition, our approach could be used to switch off nonthermal contributions in experiments, allowing reliable electron-phonon coupling constants to be obtained more easily.

47 OTHER INSTRUMENTATION↗

Dynamic Observation of Dendritic Quasicrystal Growth upon Laser-Induced Solid-State Transformation

In this paper, we report the laser-induced solid-state transformation between a periodic “approximant” and quasicrystal in the Al-Cr system during rapid quenching. Dynamic transmission electron microscopy allows us to capture in situ the dendritic growth of the metastable quasicrystals. The formation of dendrites during solid-state transformation is a rare phenomenon, which we attribute to the structural similarity between the two intermetallics. Through ab initio molecular dynamics simulations, we identify the dominant structural motif to be a 13-atom icosahedral cluster transcending the phases of matter.

36 MATERIALS SCIENCE↗

EI_MS_ML

The unambiguous identification of compounds from their electron ionization mass (EI-MS) spectra remains a significant unsolved problem in the field of metabolomics and analytical chemistry as a whole. Typically EI-MS spectra are compared using various mathematical operations that convert the spectral similarity or differences into a distance-like metric that roughly approximates the similarity of any two spectra. A commonly used metric for this is the cosine similarity metric which has values close to one for very similar spectra and a value of zero for very dissimilar spectra; however, no metric is perfect. Due to the prevalence of structurally-similar compounds such as isomers and the prevalence of certain fragmentation patterns across structurally-dissimilar compounds, the unambiguous assignment of EI-MS spectra compounds remains difficult. Frequently, querying an observed EI-MS spectrum against a large database such as the NIST17 library yields multiple possible assignments requiring the end user to distinguish between multiple high scoring hits, or multiple low scoring hits while keeping in mind that the correct hit may not be in the database at all. Although techniques such as orthogonal information from techniques such as chromatography can greatly aid in unambiguous assignment, this also requires more complicated experimental designs and access to more complicated analytical instrumentation. Substructures can be trivially detected and represented as strings using a previously published technique called node coloring from a known chemical structure. However, for experimentally-derived EI-MS spectra this information must be derived from the spectra itself (i.e., because we do not know what compound it represents). To achieve this, the software uses techniques from the field of machine learning and a large training dataset of EI-MS spectra corresponding to known structures annotated with substructure strings, to build models that can predict the presence of a given chemical substructure from an EI-MS spectrum directly.If these predictions are of high-quality (i.e., are unlikely to be false positives), the presence of one or more predicted substructures can be used to constrain the number of possible hits for a query spectrum. Mathematically, this restriction could be expressed in many forms, but the most straight-forward implementation is to weight the cosine similarity of a query spectrum and a plausible database match with a Tanimoto-like coefficient based on the ratio of the number of substructures predicted to the number of substructures present in the potential database hit. Determining which combination of models best reduces assignment ambiguity will be achieved using a combination of manual curation and optimization techniques such as genetic algorithms. This software will perform all the steps necessary to construct said models from a training dataset and evaluate them using a holdout dataset. Various statistical analyses can be performed to determine if this approach does decrease assignment ambiguity. For example, if this approach works, on average, the rank-order of the correct assignment for the holdout set of EI-MS spectra should decrease and the weighted cosine similarities for most of the possible matches in the database should be better than the unweighted cosine similarities. Furthermore, this same pipeline can be used on real experimental data to generate less ambiguous assignments.

Mitchell, Joshua↗

Crystal structure of Methanococcus jannaschii dihydroorotase

In this paper, we report the structural analysis of dihydroorotase (DHOase) from the hyperthermophilic and barophilic archaeon Methanococcus jannaschii . DHOase catalyzes the reversible cyclization of N-carbamoyl-l-aspartate to l-dihydroorotate in the third step of de novo pyrimidine biosynthesis. DHOases form a very diverse family of enzymes and have been classified into types and subtypes with structural similarities and differences among them. This is the first archaeal DHOase studied by x-ray diffraction. Its structure and comparison with known representatives of the other subtypes help define the structural features of the archaeal subtype. The M. jannaschii DHOase is found here to have traits from all subtypes. Contrary to expectations, it has a carboxylated lysine bridging the two Zn ions in the active site, and a long catalytic loop. It is a monomeric protein with a large β sandwich domain adjacent to the TIM barrel. Loop 5 is similar to bacterial type III and the C-terminal extension is long.

59 BASIC BIOLOGICAL SCIENCES↗

Quantification of Dynamic Scattering Effects in Molecular Crystals using Large Angle Rocking Beam Electron Diffraction

Electron crystallography provides a pathway to solve structure of small crystals (< 1um) in size, and thus overcomes difficult synthesis constraints involved in growing large crystals. Generally, electron diffraction data is collected in the form of integrated intensity using continuous rotation or by precession. The measured intensities in 3D are utilized for structure solution. Using this approach, structure solution of difficult crystals, such as small crystals of zeolites, metal-organic frameworks, molecular crystals, and proteins , can be solved by electron diffraction. However, electron structure solutions are regularly reported with higher Rvalues than x-ray or neutron diffraction. While similar structures are found despite the high R-values, the differences in the measure intensity and theory calculated intensity limit information that can be extracted by electron diffraction. Previous work demonstrated that including multiple-scattering effects significantly reduce the R-values . Thus, it is critical to be able to quantify the dynamical diffraction effects in molecular crystals.

Crystallography↗

Structure–property relations of binary ferrite melts

Molten ferrite systems are used in the smelting and refining processes in steelmaking, to reduce the loss of metals in slags and to accelerate reaction rates. Here, high-energy x-ray diffraction experiments have been performed on aerodynamically levitated molten spheres of 43BaO–57FeO X and 43SrO–57FeO X at 1873 K using laser beam heating. The composition was varied within the range of x = 1–1.5 by changing the oxygen partial pressure of the levitation gas. The corresponding x-ray pair distribution functions have been interpreted using empirical potential structure refinement (EPSR) modeling. In oxygen-rich melts (x = 1.5), our EPSR models indicate very similar structures for the different alkaline-earth liquids, with both the Ba–O and Sr–O coordination numbers to be ∼8.4 and the total Fe–O coordination numbers ∼5.7. However, our models show that in reducing environments, the Fe 3+ and Fe 2+ ions exhibit very different behaviors in the Ba- and Sr-ferrite liquids. In the Ba-ferrite melt, the Fe 3+ –O coordination number decreases from 5.7 (at x = 1.5) to 5.2 (at x = 1.07), whereas Fe 2+ –O remains constant at ∼5.0 across the same compositional range. In the Sr melts, both the Fe 2+ –O and Fe 3+ –O coordination numbers rise from ∼5.7 (at x = 1.5) to 6.3 (at x = 1.07). All models show the structures to be heterogeneous with intertwined nanometer sized clusters or channels of Ba/Sr–O and Fe–O polyhedra that grow as oxygen content is reduced. Changes in the viscosity and electrical properties are interpreted in terms of the number of bridging and non-bridging oxygens associated with FeO 4 tetrahedra and concentration of charge carriers, respectively.

Benmore, Chris J. [Argonne National Laboratory (AN↗

First-order structural phase transition at low temperature in GaPt 5 P and its rapid enhancement with pressure

Single crystals of X Pt 5 ⁢P (X = Al, Ga, and In), belonging to the 1-5-1 family of compounds, were grown from a Pt-P solution at high temperatures, and measurements of the ambient pressure, temperature-dependent magnetization, resistivity, and x-ray diffraction were made. Additionally, the ambient-pressure Hall resistivity and temperature-dependent resistance under pressure were measured on GaPt 5 ⁢P. All three compounds have a tetragonal P4/mmm crystal structure at room temperature with metallic transport and weak diamagnetism over the 2–300 K temperature range. Surprisingly, at ambient pressure, both the transport and magnetization measurements on GaPt 5 ⁢P show a steplike feature in the 70–90 K region, suggesting a possible structural phase transition. Neither AlPt 5 ⁢P nor InPt 5 ⁢P have any signatures of a phase transition in their temperature-dependent electrical resistance and magnetization data. Both the hysteretic nature and sharpness of the features in the GaPt 5 ⁢P data suggest that the transition is first-order. Further, single-crystal x-ray diffraction measurements provided further details of the structural transition with a possibility of a crystal symmetry different from P⁢4/mmm below the transition temperature. The transition is characterized by anisotropic changes in the lattice parameters and a volume collapse with respect to the high-temperature tetragonal crystal structure. Furthermore, satellite peaks are observed at two distinct and nonequivalent wave vectors (0, 0, 0.5) and (0.5, 0.5, 0.5), and density functional theory calculations present phonon softening, especially at (0.5, 0.5, 0.5), as a possible driving mechanism. Additionally, we find that the structural transition temperature increases rapidly with increasing pressure, reaching room temperature by ~2.2 GPa, highlighting the high degree of pressure sensitivity of GaPt 5 ⁢P and fragile nature of its room-temperature structure. Even though the volume collapse and extreme pressure sensitivity suggest chemical pressure should drive a similar structural change in AlPt 5⁢ P, where both unit-cell dimensions and volume are smaller, its structure is found to be the same as that of the room-temperature GaPt 5 ⁢P. Overall, GaPt 5 ⁢P stands out as a sole member of the 1-5-1 family of compounds for which a temperature-driven structural change has been observed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Unique Structural Features Relate to Evolutionary Adaptation of Cytochrome P450 in the Abyssal Zone

Cytochromes P450 (CYPs) form one of the largest enzyme superfamilies, with similar structural folds yet biological functions varying from synthesis of physiologically essential compounds to metabolism of myriad xenobiotics. Sterol 14α-demethylases (CYP51s) represent a very special P450 family, regarded as a possible evolutionary progenitor for all currently existing P450s. In metazoans CYP51 is critical for the biosynthesis of sterols including cholesterol. Here we determined the crystal structures of ligand-free CYP51s from the abyssal fish Coryphaenoides armatus and human-. Comparative sequence–structure–function analysis revealed specific structural elements that imply elevated conformational flexibility, uncovering a molecular basis for faster catalytic rates, lower substrate selectivity, and intrinsic resistance to inhibition. In addition, the C. armatus structure displayed a large-scale repositioning of structural segments that, in vivo, are immersed in the endoplasmic reticulum membrane and border the substrate entrance (the FG arm, >20 Å, and the β4 hairpin, >15 Å). The structural distinction of C. armatus CYP51, which is the first structurally characterized deep sea P450, suggests stronger involvement of the membrane environment in regulation of the enzyme function. We interpret this as a co-adaptation of the membrane protein structure with membrane lipid composition during evolutionary incursion to life in the deep sea.

Biochemistry & Molecular Biology↗

ACES-GNN: can graph neural network learn to explain activity cliffs?

Graph Neural Networks (GNNs) have revolutionized molecular property prediction by leveraging graph-based representations, yet their opaque decision-making processes hinder broader adoption in drug discovery. This study introduces the Activity-Cliff-Explanation-Supervised GNN (ACES-GNN) framework, designed to simultaneously improve predictive accuracy and interpretability by integrating explanation supervision for activity cliffs (ACs) into GNN training. ACs, defined by structurally similar molecules with significant potency differences, pose challenges for traditional models due to their reliance on shared structural features. By aligning model attributions with chemist-friendly interpretations, the ACES-GNN framework bridges the gap between prediction and explanation. Validated across 30 pharmacological targets, ACES-GNN consistently enhances both predictive accuracy and attribution quality for ACs compared to unsupervised GNNs. Our results demonstrate a positive correlation between improved predictions and accurate explanations, offering a robust and adaptable framework to better understand and interpret ACs. This work underscores the potential of explanation-guided learning to advance interpretable artificial intelligence in molecular modeling and drug discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Heavy boron doping in superconducting carbon materials

Here we examine physical properties of heavily boron-doped sp 3 -hybridized carbon allotropes: cubic diamond, hexagonal diamond, and body centered tetragonal C 4 . The structural similarity between cubic diamond and hexagonal diamond leads to similar responses to substitutional boron doping. On the other hand, body centered tetragonal C 4 exhibits distinct structural and electronic properties because of its characteristic structure. Our study also shows that the superconducting transition temperatures up to 60 K are possible in heavily doped carbon materials despite their various atomistic structures.

36 MATERIALS SCIENCE↗

Structures of five salt forms of disulfonated monoazo dyes

The structures of five s -block metal salt forms of three disulfonated monoazo dyes are presented. These are poly[di-μ-aqua-diaqua[μ 4 -3,3'-(diazane-1,2-diyl)bis(benzenesulfonato)]disodium(I)], [Na 2 (C 12 H 8 N 2 O 6 S 2 )(H 2 O) 4 ] n , (I), catena -poly[[tetraaquacalcium(II)]-μ-3,3'-(diazane-1,2-diyl)bis(benzenesulfonato)], [Ca(C 12 H 8 N 2 O 6 S 2 )(H 2 O) 4 ] n , (II), catena -poly[[[diaquacalcium(II)]-μ-2-(4-amino-3-sulfonatophenyl)-1-(4-sulfonatophenyl)diazenium] dihydrate], {[Na(C 12 H 10 N 3 O 6 S 2 )(H 2 O) 2 ]·2H 2 O} n , (III), hexaaquamagnesium bis[2-(4-amino-3-sulfonatophenyl)-1-(4-sulfonatophenyl)diazenium] octahydrate, [Mg(H 2 O) 6 ](C 12 H 10 N 3 O 6 S 2 ) 2 ·8H 2 O, (IV), and poly[[{μ 2 -4-[2-(4-amino-2-methyl-5-methoxyphenyl)diazen-1-yl]benzene-1,3-disulfonato}di-μ-aqua-diaquabarium(II)] dihydrate], {[Ba(C 14 H 13 N 3 O 7 S 2 )(H 2 O) 4 ]·2H 2 O} n , (V). Compound (III) is that obtained on crystallizing the commercial dyestuff Acid Yellow 9 [74543-21-8]. The Mg species is a solvent-separated ion-pair structure and the others are all coordination polymers with bonds from the metal atoms to sulfonate groups. Compound (I) is a three-dimensional coordination polymer, (V) is a two-dimensional coordination polymer and both (II) and (III) are one-dimensional coordination polymers. The coordination behaviour of the azo ligands and the water ligands, the dimensionality of the coordination polymers and the overall packing motifs of these five structures are contrasted to those of monosulfonate monoazo congers. It is found that (I) and (II) adopt similar structural types to those of monosulfonate species but that the other three structures do not.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗