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At least 199 records · Page 11

Sputter-Deposited Mo Thin Films: Multimodal Characterization of Structure, Surface Morphology, Density, Residual Stress, Electrical Resistivity, and Mechanical Response

Multimodal datasets of materials are rich sources of information which can be leveraged for expedited discovery of process–structure–property relationships and for designing materials with targeted structures and/or properties. For this data descriptor article, we provide a multimodal dataset of magnetron sputter-deposited molybdenum (Mo) thin films, which are used in a variety of industries including high temperature coatings, photovoltaics, and microelectronics. In this dataset we explored a process space consisting of 27 unique combinations of sputter power and Ar deposition pressure. Here, the phase, structure, surface morphology, and composition of the Mo thin films were characterized by x-ray diffraction, scanning electron microscopy, atomic force microscopy, and Rutherford backscattering spectrometry. Physical properties—namely, thickness, film stress and sheet resistance—were also measured to provide additional film characteristics and behaviors. Additionally, nanoindentation was utilized to obtain mechanical load-displacement data. The entire dataset consists of 2072 measurements including scalar values (e.g., film stress values), 2D linescans (e.g., x-ray diffractograms), and 3D imagery (e.g., atomic force microscopy images). An additional 1889 quantities, including film hardness, modulus, electrical resistivity, density, and surface roughness, were derived from the experimental datasets using traditional methods. Minimal analysis and discussion of the results are provided in this data descriptor article to limit the authors’ preconceived interpretations of the data. Overall, the data modalities are consistent with previous reports of refractory metal thin films, ensuring that a high-quality dataset was generated. The entirety of this data is committed to a public repository in the Materials Data Facility.

36 MATERIALS SCIENCE↗

Impact of Water Extraction on Malonamide Aggregation: A Molecular Dynamics and Graph Theoretic Approach

Solution structure in liquid-liquid extraction affects the efficacy of separation; however, even for simplified organic phases, structural characterization and attribution of aggregation to intermolecular interactions are fundamental challenges. We investigate water uptake into organic phases for two malonamides commonly applied to actinide and lanthanide separations. Extracted water induces reorganization of the amphiphilic extractant molecules, although we find this rearrangement is not strongly manifested in small-angle X-ray scattering making it challenging to probe without methods such as atomistic simulation. Using a graph theoretic approach to define hydrogen bonded water/malonamide aggregates from molecular dynamics simulations, we find evidence of a characteristic aggregate size by water number that results from geometric accommodation of the surrounding malonamide molecules. Furthermore, this implies a degree of size selectivity inherent to these water-in-oil aggregates. Conversely, we find no evidence of a characteristic size of the aggregates with respect to their malonamide number. By defining a separate graphical representation of self-association of the amphiphilic malonamides, we quantify how water affects the local and nonlocal topology of the malonamide network, providing a basis for characterization of the structure and impact of polar solutes in increasingly complex organic phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular Origins of Temperature-Dependent X-ray Absorption in YAG:Dy

The absorption and emission of X-rays in dysprosium-doped yttrium aluminum garnet (YAG:Dy) has produced unexpected thermographic behavior, which is investigated using a combination of finite temperature ab initio molecular dynamic simulations, structural characterization, and electronic structure calculations of X-ray characteristics. Calculated average peak X-ray absorption spectra (XAS) from simulations between 300 and 600 K result in peak intensity loss due to thermalization effects, matching experimentally measured behavior of YAG:Dy. Here, investigation of atomic snapshots indicates structural factors that correlated with the X-ray behavior, with the first Y–O coordination sphere identified as the primary structural feature unique to high XAS intensity as calculated by radial and pair distribution functions.

Ab initio molecular dynamics↗

Effects of Al:Si and (Al+Na):Si Ratios on the Properties of the International Simple Glass, Part II: Structure

High-alumina containing high-level waste (HLW) will be vitrified at the Waste Treatment Plant at the Hanford Site. The resulting glasses, high in alumina, will have distinct composition-structure-property (C-S-P) relationships compared to previously studied HLW glasses. These C-S-P relationships determine the processability and product durability of glasses and therefore must be understood. The main purpose of this study is to understand the detailed structural changes caused by Al:Si and (Al+Na):Si substitutions in a simplified nuclear waste model glass (ISG, International Simple Glass) by combining experimental structural characterizations and molecular dynamics (MD) simulations. The structures of these two series of glasses were characterized by neutron total scattering and 27Al, 23Na, 29Si, and 11B solid-state nuclear magnetic resonance (NMR) spectroscopy. Additionally, MD simulations were used to generate atomistic structural models of the borosilicate glasses and simulation results were validated by the experimental structural data. Short-range (e.g., bond distance, coordination number, etc.) and medium-range (e.g., oxygen speciation, network connectivity, polyhedral linkages) structural features of the borosilicate glasses were systematically investigated as a function of the degree of substitution. The results show that bond distance and coordination number of the cation-oxygen pairs are relatively insensitive to Al:Si and (Al+Na):Si substitutions with the exception of the B-O pair. Additionally, the Al:Si substitution results in an increase of tri-bridging oxygen species, while (Al+Na):Si substitution creates non-bridging oxygen species. Charge compensator preferences were found for Si-[NBO] (Na+), [3]B-[NBO] (Na+), [4]B (mostly Ca2+), [4]Al (nearly equally split Na+ and Ca2+), and [6]Zr (mostly Ca2+). The network former-BO-network former linkages preferences were also tabulated; Si-O-Al and Al-O-Al were preferred at the expense of lower Si-O-[3]B and [3]B-O-[3]B linkages. These results provide insights on the structural origins of property changes such as glass transition temperature caused by the substitutions, providing a basis for future improvements of theoretical and computer simulation models.

Lu, Xiaonan↗

Data-centric framework for crystal structure identification in atomistic simulations using machine learning

Atomic-level modeling performed at large scales enables the investigation of mesoscale materials properties with atom-by-atom resolution. The spatial complexity of such cross-scale simulations renders them unsuitable for simple human visual inspection. Instead, specialized structure characterization techniques are required to aid interpretation. These have historically been challenging to construct, requiring significant intuition and effort. Here we propose an alternative framework for a fundamental structural characterization task: classifying atoms according to the crystal structure to which they belong. Our approach is data-centric and favors the employment of Machine Learning over heuristic rules of classification. A group of data-science tools and simple local descriptors of atomic structure are employed together with an efficient synthetic training set. We also introduce the first standard and publicly available benchmark data set for evaluation of algorithms for crystal-structure classification. Further, it is demonstrated that our data-centric framework outperforms all of the most popular heuristic methods—especially at high temperatures when lattices are the most distorted—while introducing a systematic route for generalization to new crystal structures. Moreover, through the use of outlier detection algorithms our approach is capable of discerning between amorphous atomic motifs (i.e., noncrystalline phases) and unknown crystal structures, making it uniquely suited for exploratory materials synthesis simulations.

36 MATERIALS SCIENCE↗

Rational design of a uranyl metal-organic framework for the capture and colorimetric detection of organic dyes

A new uranyl containing metal-organic framework, RPL-1: [(UO2)2(C28H18O8)] · H2O (RPL for Radiochemical Processing Laboratory), was prepared, structurally characterized, and the solid-state photoluminescence properties explored. The single crystal X-ray diffraction data reveal the structure of RPL-1 consists of two crystallographically unique three dimensional, interpenetrating nets with a 4,3-connected tbo topology. Each net contains large pores with an average width of 22.8 Å and is formed from monomeric, hexagonal bipyramidal uranyl nodes that are linked via 1,2,4,5-tetrakis(4-carboxyphenyl)benzene (TCPB) linkers. The thermal and photophysical properties of RPL-1 were investigated using thermogravimetric analysis and absorbance, fluorescence, and lifetime spectroscopies. The material displays excellent thermal stability and temperature dependent uranyl and TCBP luminescence. The framework is stable in aqueous media and due to the large void space (constituting 76% of the unit cell by volume) can sequester organic dyes, the uptake of which induces a visible change to the color of the material.

Surbella, Robert G.↗

Functional Characterization and Structural Insights Into Stereoselectivity of Pulegone Reductase in Menthol Biosynthesis

Monoterpenoids are the main components of plant essential oils and the active components of some traditional Chinese medicinal herbs like Mentha haplocalyx Briq ., Nepeta tenuifolia Briq ., Perilla frutescens (L.) Britt and Pogostemin cablin (Blanco) Benth. Pulegone reductase is the key enzyme in the biosynthesis of menthol and is required for the stereoselective reduction of the Δ 2,8 double bond of pulegone to produce the major intermediate menthone, thus determining the stereochemistry of menthol. However, the structural basis and mechanism underlying the stereoselectivity of pulegone reductase remain poorly understood. In this study, we characterized a novel (-)-pulegone reductase from Nepeta tenuifolia ( Nt PR), which can catalyze (-)-pulegone to (+)-menthone and (-)-isomenthone through our RNA-seq, bioinformatic analysis in combination with in vitro enzyme activity assay, and determined the structure of (+)-pulegone reductase from ( Mp PR) by using X-ray crystallography, molecular modeling and docking, site-directed mutagenesis, molecular dynamics simulations, and biochemical analysis. We identified and validated the critical residues in the crystal structure of Mp PR involved in the binding of the substrate pulegone. We also further identified that residues Leu56, Val282, and Val284 determine the stereoselectivity of the substrate pulegone, and mainly contributes to the product stereoselectivity. This work not only provides a starting point for the understanding of stereoselectivity of pulegone reductases, but also offers a basis for the engineering of menthone/menthol biosynthetic enzymes to achieve high-titer, industrial-scale production of enantiomerically pure products.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Characterization and structure of the human lysine-2-oxoglutarate reductase domain, a novel therapeutic target for treatment of glutaric aciduria type 1

In humans, a single enzyme 2-aminoadipic semialdehyde synthase (AASS) catalyses the initial two critical reactions in the lysine degradation pathway. This enzyme evolved to be a bifunctional enzyme with both lysine-2-oxoglutarate reductase (LOR) and saccharopine dehydrogenase domains (SDH). Moreover, AASS is a unique drug target for inborn errors of metabolism such as glutaric aciduria type 1 that arise from deficiencies downstream in the lysine degradation pathway. While work has been done to elucidate the SDH domain structurally and to develop inhibitors, neither has been done for the LOR domain. Here, we purify and characterize LOR and show that it is activated by alkylation of cysteine 414 by N-ethylmaleimide. We also provide evidence that AASS is rate-limiting upon high lysine exposure of mice. Finally, we present the crystal structure of the human LOR domain. Our combined work should enable future efforts to identify inhibitors of this novel drug target.

59 BASIC BIOLOGICAL SCIENCES↗

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↗

Graph-Directed Approach for Downselecting Toxins for Experimental Structure Determination

Conotoxins are short, cysteine-rich peptides of great interest as novel therapeutic leads and of great concern as lethal biological agents due to their high affinity and specificity for various receptors involved in neuromuscular transmission. Currently, of the approximately 6000 known conotoxin sequences, only about 3% have associated structural characterization, which leads to a bottleneck in rapid high-throughput screening (HTS) for identification of potential leads or threats. In this work, we combine a graph-based approach with homology modeling to expand the library of conotoxin structures and to identify those conotoxin sequences that are of the greatest value for experimental structural characterization. The latter would allow for the rapid expansion of the known structural space for generating high quality template-based models. Our approach generalizes to other evolutionarily-related, short, cysteine-rich venoms of interest. Overall, we present and validate an approach for venom structure modeling and experimental guidance and employ it to produce a 290%-larger library of approximate conotoxin structures for HTS. We also provide a set of ranked conotoxin sequences for experimental structure determination to further expand this library.

59 BASIC BIOLOGICAL SCIENCES↗

A Computational Study of RNA Tetraloop Thermodynamics, Including Misfolded States

An important characteristic of RNA folding is the adoption of alternative configurations of similar stability, often referred to as misfolded configurations. These configurations are considered to compete with correctly folded configurations, although their rigorous thermodynamic and structural characterization remains elusive. Tetraloop motifs found in large ribozymes are ideal systems for an atomistically detailed computational quantification of folding free energy landscapes and the structural characterization of their constituent free energy basins, including nonnative states. In this work, we studied a group of closely related 10-mer tetraloops using a combined parallel tempering and metadynamics technique that allows a reliable sampling of the free energy landscapes, requiring only knowledge that the stem folds into a canonical A-RNA configuration. Here we isolated and analyzed unfolded, folded, and misfolded populations that correspond to different free energy basins. We identified a distinct misfolded state that has a stability very close to that of the correctly folded state. This misfolded state contains a predominant population that shares the same structural features across all tetraloops studied here and lacks the noncanonical A-G base pair in its loop portion. Further analysis performed with biased trajectories showed that although this competitive misfolded state is not an essential intermediate, it is visited in most of the transitions from unfolded to correctly folded states. Moreover, the tetraloops can transition from this misfolded state to the correctly folded state without requiring extensive unfolding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure and Stability of the Iodide Elpasolite, Cs 2 AgBiI 6

Iodide elpasolites (or double perovskites, A 2 B'B"I 6 , B' = M + , B" = M 3+ ) are predicted to be promising alternatives to lead-based perovskite semiconductors for photovoltaic and optoelectronic applications, but no iodide elpasolite has ever been definitively prepared or structurally characterized. Iodide elpasolites are widely predicted to be unstable due to favorable decomposition to the competing A 3 B 2 I 9 (B = M 3+ ) phase. Here, we report the results of synchrotron XRD and X-ray total scattering measurements on putative Cs 2 AgBiI 6 nanocrystals made via anion exchange from parent Cs 2 AgBiBr 6 nanocrystals. Rietveld refinement of XRD and PDF data shows that these nanocrystals indeed exhibit a tetragonal ($I$$\overline{4}$$m$) elpasolite structure, making them the first example of a structurally characterized iodide elpasolite. In conclusion, a series of experiments probing structural relaxation and the effects of surface ligation or grain size all point to the critical role of surface free energy in stabilizing the iodide elpasolite phase in these nanocrystals.

36 MATERIALS SCIENCE↗

Simultaneously upgrading CO 2 and light alkanes into value-added products

We will discuss recent results from our group in reacting CO 2 and light alkanes to produce syngas, olefins, aromatics, and oxygenates. We will mainly use the simultaneous upgrading of CO 2 and ethane (SU-CO 2 Et) as examples to demonstrate the feasibility and reaction pathways of these processes. We will briefly discuss synthesis methods and essential structural characterization techniques that can be applied to SU-CO 2 Et catalysts. We will then illustrate how to identify and apply distinct active sites for different upgrading processes, using a combination of kinetic studies, in situ characterization, and density functional theory (DFT) calculations. We will conclude the Perspective by pointing out challenges and potential directions in catalyst design and synthesis, as well as structural characterization and mechanistic investigations, to further advance the simultaneous upgrading of CO 2 and light alkanes.

03 NATURAL GAS↗

Photoinduced reversible phase transition in a phenothiazine-based metal-organic framework

Photoinduced phase transitions in metal-organic frameworks are provoked by structural changes of photoresponsive linkers within the framework under light irradiation. These transitions are rare but fundamentally important as they can bring about light-switchability on a variety of properties of the materials. In this work, phenothiazine as a photoresponsive unit with distinctive photochemical properties is incorporated into a Zn-based metal-organic framework, PCN-401. The structural characterization of PCN-401 revealed a reversible structural transition upon light irradiation. The mechanisms behind the photoinduced phase transition are studied systematically by spectrometric methods and structural stability characterization. Our mechanistic studies successfully showcased how the phenothiazine unit in the framework undergoes structural transformation under light irradiation and how the reversible phase transition leads to the property changes. The findings have emphasized the significance of phenothiazine in photoresponsive materials and can serve as inspiration for the design and understandings of next-generation photoresponsive metal-organic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural validation of a thermoplastic composite wind turbine blade with comparison to a thermoset composite blade

Reactive infusible thermoplastics have the potential to be advantageous for wind turbine blade composites because they are recyclable at end of life, can have reduced manufacturing costs, enable thermal joining and have similar, and in some cases better, structural properties than traditional thermoset epoxy composites. However, these materials are new to the wind industry and there is risk to investing in a material that has not been validated at a blade scale. Industry cannot adopt a new material such as this without large-scale validation and demonstration of system-level advantages in cost and/or performance. This paper presents structural characterization of a 13-m thermoplastic composite wind turbine blade compared to an identical geometry thermoset epoxy blade. In this work, the results of this comparison showed that the flatwise structural static performance and the fatigue performance of the two blades were similar, but the thermoplastic composite blade had increased damping compared to the epoxy blade, which may result in reduced operational loads.

17 WIND ENERGY↗

Sequence-structure-function characterization of the emerging tetracycline destructase family of antibiotic resistance enzymes

Tetracycline destructases (TDases) are flavin monooxygenases which can confer resistance to all generations of tetracycline antibiotics. The recent increase in the number and diversity of reported TDase sequences enables a deep investigation of the TDase sequence-structure-function landscape. Here, we evaluate the sequence determinants of TDase function through two complementary approaches: (1) constructing profile hidden Markov models to predict new TDases, and (2) using multiple sequence alignments to identify conserved positions important to protein function. Using the HMM-based approach we screened 50 high-scoring candidate sequences in Escherichia coli, leading to the discovery of 13 new TDases. The X-ray crystal structures of two new enzymes from Legionella species were determined, and the ability of anhydrotetracycline to inhibit their tetracycline-inactivating activity was confirmed. Using the MSA-based approach we identified 31 amino acid positions 100% conserved across all known TDase sequences. The roles of these positions were analyzed by alanine-scanning mutagenesis in two TDases, to study the impact on cell and in vitro activity, structure, and stability. These results expand the diversity of TDase sequences and provide valuable insights into the roles of important residues in TDases, and flavin monooxygenases more broadly.

60 APPLIED LIFE SCIENCES↗

Characterizing Structure-Dependent TiS 2 /Water Interfaces Using Deep-Neural-Network-Assisted Molecular Dynamics

As a promising layered electrode material, TiS 2 -based capacitive deionization (CDI) devices for water desalination have attracted significant attention. However, TiS 2 /H 2 O interfacial features, potentially important for device optimization, remain unidentified. Using Deep Potential Molecular Dynamics (DPMD), we characterized distinct aqueous interfaces introduced by four TiS 2 terminations expected to be present as water intercalates into TiS 2 , namely, Armchair, Zigzag, Zigzag-L, and Zigzag-R. First, we assessed important representative physical properties of the system to validate the deep potentials (DPs). DPMD simulations agree well with experiments and first-principles simulations, suggesting the DPs are accurate and reliable. Subsequent simulations of these TiS 2 /water interfaces revealed how TiS 2 surface termination influences the structure of interfacial water. This effect is most evident in the first and second water layers close to the TiS 2 surface, and more pronounced when spontaneous dissociative adsorption of water occurs. The extent of water dissociation on each surface was evaluated using enhanced sampling. Zigzag-L is the only interface where proton transfer from adsorbed water to TiS 2 surface S atoms is thermodynamically and kinetically favored. The coexistence of surface four-fold-coordinated Ti (Ti 4c ) and one-fold-coordinated S (S 1c ) is found to be essential to making proton transfer feasible on the Zigzag-L surface. Furthermore, remaining unprotonated S 1c atoms can act as good proton acceptors after water dissociation. Thus, TiS 2 with Zigzag-L termination may be a surface to avoid in CDI device construction, given that pH fluctuations adversely affect performance. Furthermore, this work provides new understanding of TiS 2 /H 2 O interfacial features that could aid future design and optimization of TiS 2 -based CDI devices for water desalination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Machine Learning Framework for Characterizing Processing–Structure Relationship in Block Copolymer Thin Films

The morphology of block copolymers (BCPs) critically influences material properties and applications. This work introduces a machine learning (ML)-enabled, high-throughput framework for analyzing grazing incidence small-angle X-ray scattering (GISAXS) data and atomic force microscopy (AFM) images to characterize BCP thin film morphology. A convolutional neural network was trained to classify AFM images by surface features, achieving 97% testing accuracy. Classified images were then analyzed to extract 2D grain size measurements from the samples in a high-throughput manner. ML models were trained to predict domain orientation based on processing parameters such as solvent ratio, additive type, and additive ratio. GISAXS-based properties were predicted with strong performances (R 2 > 0.75), while AFM-based property predictions were less accurate (R 2 < 0.60), likely due to the localized nature of AFM measurements compared to the bulk information captured by GISAXS. Beyond model performance, interpretability was addressed using SHapley Additive exPlanations (SHAP). SHAP analysis revealed that the additive ratio had the largest impact on morphological predictions, where additive provides the BCP chains with increased volume to rearrange into thermodynamically favorable morphologies. This interpretability helps validate model predictions and offers insight into parameter importance. Altogether, the presented framework combining high-throughput characterization and interpretable ML offers an approach to exploring and optimizing BCP thin film morphology across a broad processing landscape.

36 MATERIALS SCIENCE↗