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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data.

3D visualization↗
DOE OSTI2018

A Two-Fold Structural Classification Method for Determining the Accurate Ensemble of Protein Structures

Atomic-level structural characterization of flexible proteins, such as intrinsically disordered proteins and multi-domain proteins connected by flexible linkers, is challenging as they possess distinct conformations in physiological conditions. Significant efforts have been made to develop integrated approaches by combining small angle neutron/X-ray scattering experiments with molecular simulations to reveal the distinct atomic structures and the corresponding populations for these flexible proteins. One widely used method, the basis-set supported ensemble method, classifies the simulation-generated protein conformations into a set of structural basis and then derives the corresponding populations by fitting to the experimental data. This method makes an implicit assumption that protein conformations of similar structures have similar small angle scattering profiles.The present work demonstrates that, for various protein systems ranging from compact globular proteins and flexible multidomain proteins through to intrinsically disordered proteins, this method provides inaccurate assessment of the structural ensemble of the protein molecules due to the breakdown of the assumption made. To alleviate this problem, a two-fold-clustering method is developed to cluster the simulation-generated protein structures using information on both 3D structure and scattering profiles. As benchmarked by both simulation and experimental results, this new method yields much more accurate populations of structural basis of protein molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A quantitative study of the structure-activity relationship in hierarchical zeolites using liquid-phase reactions

Micro/meso/macroporous (hierarchical) zeolites show remarkable catalytic performance for reactions involving bulky reactants. However, quantitative assessment of the microstructural characteristics contributing to the observed performance remains elusive. Here, structure–activity relationships are established for a set of micro/mesoporous self-pillared pentasil (SPP) zeolites using two parallel liquid-phase reactions (benzyl alcohol alkylation and self-etherification) based on analysis of mass transport and reaction kinetics. A reaction–diffusion mathematical model is developed that quantitatively assigns the catalytic contributions of the external surface and micropores of SPP zeolites for these reactions. In addition, the effect of the zeolite external surface structure on the corresponding catalytic activity is quantitatively assessed by comparing SPP zeolites (with MFI structure) with MCM-22 (with MWW structure). This work demonstrates that reaction–diffusion modeling allows quantitative description of the catalytic performance of hierarchical zeolites and provides a model reaction to assess nm-sized characteristic diffusion lengths in MFI.

bio-inspired↗
DOE OSTI2021

Global Optimization of Chemical Cluster Structures: Methods, Applications, and Challenges

Chemical clusters are relevant to many applications in catalysis, separations, materials, and energy sciences. Experimentally, the structure of clusters is difficult to determine, but it is very important in understanding their chemistry and properties. Computational methods can be used to examine cluster structure, however finding the most stable structure is not simple, particularly as the cluster size increases. Global optimization techniques have long been used to tackle the problem of the most stable structure, but such approaches would have to look for a global minimum, while sampling local minima over the whole potential energy surface as well. In this review, the state-of-the-art theory of global optimization theory is summarized. First, the definition, significance, relation to experiments, and a brief history of global optimization is presented. We then discuss, in more detail, three versatile global optimization methods: the basin hopping, the artificial bee colony algorithm, and the genetic algorithm. We close with some representative application examples of global optimization of clusters since 2016 and the challenges, open questions and opportunities in this field.

Global optimization, Chemical clusters, Artificial↗
DOE OSTI2015

Making structured metals transparent for ultrabroadband electromagnetic waves and acoustic waves

In this review, we present our recent work on making structured metals transparent for broadband electromagnetic waves and acoustic waves via excitation of surface waves. First, we theoretically show that one-dimensional metallic gratings can become transparent and completely antireflective for extremely broadband electromagnetic waves by relying on surface plasmons or spoof surface plasmons. Second, we experimentally demonstrate that metallic gratings with narrow slits are highly transparent for broadband terahertz waves at oblique incidence and high transmission efficiency is insensitive to the metal thickness. Further, we significantly develop oblique metal gratings transparent for broadband electromagnetic waves (including optical waves and terahertz ones) under normal incidence. In the third, we find the principles of broadband transparency for structured metals can be extended from one-dimensional metallic gratings to two-dimensional cases. Moreover, similar phenomena are found in sonic artificially metallic structures, which present the transparency for broadband acoustic waves. These investigations provide guidelines to develop many novel materials and devices, such as transparent conducting panels, antireflective solar cells, and other broadband metamaterials and stealth technologies. - Highlights: • Making structured metals transparent for ultrabroadband electromagnetic waves. • Non-resonant excitation of surface plasmons or spoof surface plasmons. • Sonic artificially metallic structures transparent for broadband acoustic waves.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography

We report that angiotensin II type 1 receptor (AT 1 R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT 1 R blockers (ARBs), the structural basis for AT 1 R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT 1 R in complex with its selective antagonist ZD7155 at 2.9 Å resolution. The AT 1 R-ZD7155 complex structure revealed key structural features ofAT 1 R and critical interactions for ZD7155 binding. Finally, docking simulations of the clinically used ARBs into the AT 1 R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT 1 R structure-function relationship and structure-based drug design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Application of micro X-ray diffraction to investigate the reaction products formed by the alkali–silica reaction in concrete structures

Alkali–silica reaction (ASR) is one of the most important deterioration mechanisms in concrete leading to substantial damages of structures worldwide. Synchrotron-based micro-X-ray diffraction (micro-XRD) was employed to characterize the mineral phases formed in micro-cracks of concrete aggregates as a consequence of ASR. This high spatial resolution technique enables to directly gain structural information on ASR products formed in a 40-year old motorway bridge damaged due to ASR. Micro-X-ray-fluorescence was applied on thin sections to locate the reaction products formed in veins within concrete aggregates. Micro-XRD pattern were collected at selected points of interest along a vein by rotating the sample. Rietveld refinement determined the structure of the ASR product consisting of a new layered framework similar to mountainite and rhodesite. It is conceivable that understanding the structure of the ASR product may help developing new technical treatments inhibiting ASR.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Monte Carlo Simulation of Borosilicate Glass Dissolution using Molecular Dynamics-Generated Glass Structures

Atomic-scale insights into the dissolution mechanisms of borosilicate glasses are critical to the development of the waste form corrosion models that inform performance assessments of nuclear waste disposal facilities. Monte Carlo (MC) simulations have been instrumental in advancing the state of knowledge of borosilicate glass dissolution; however, all such simulations to date have relied on lattices to represent the amorphous glass structure, thereby potentially introducing artifacts. Therefore, a new approach, referred to as the amorphous MC approach, has been developed whereby glass structures generated from molecular dynamics simulations are used as starting points for MC simulations of glass dissolution. MC simulations of sodium borosilicate glasses that covered a wide compositional range were performed and revealed correlations between dissolution rate and structural features of the glasses. Notably, the lattice MC approach predicted the fraction of tetrahedral boron to have a lesser influence on the dissolution rate than computed with the amorphous MC approach. The lattice MC simulations also overestimated the dissolution rate for a given glass composition. These findings highlight the importance of using truly amorphous structures in MC simulations of glass corrosion.

Kerisit, Sebastien N.↗
DOE OSTI2014

Magnetic structures of β{sub I}-Li{sub 2}CoSiO{sub 4} and γ{sub 0}-Li{sub 2}MnSiO{sub 4}: Crystal structure type vs. magnetic topology

The magnetic structure and properties of the candidate lithium-ion battery cathode materials Pbn2{sub 1}(≡Pna2{sub 1}) Li{sub 2}CoSiO{sub 4} and P2{sub 1}/n Li{sub 2}MnSiO{sub 4} have been studied experimentally using low-temperature neutron powder diffraction and magnetometry. Both materials undergo long-range antiferromagnetic ordering, at 14 K and 12 K respectively, due to super–super-exchange mediated by bridging silicate groups. Despite having different crystal structures (wurtzite- vs. “dipolar”-type), Li{sub 2}CoSiO{sub 4} and Li{sub 2}MnSiO{sub 4} have the same topology in terms of magnetic interactions, and adopt collinear magnetic structures of the same type with the propagation vectors (0, 1/2, 1/2) and (1/2, 0, 1/2), respectively. The magnetic moments in the two materials are aligned in parallel and obliquely to the distorted closed-packed layers of oxygen atoms. The experimentally observed values of the ordered magnetic moments, 2.9 μ{sub B} and 4.6 μ{sub B}, are close to those expected for d{sup 7} Co{sup 2+} and d{sup 5} Mn{sup 2+}, respectively. - Graphical abstract: Despite the different crystal structures β{sub I}-Li{sub 2}CoSiO{sub 4} and γ{sub 0}-Li{sub 2}MnSiO{sub 4} have similar magnetic topology and as a result adopt magnetic structure of the same type. - Highlights: • Magnetic structures of Li{sub 2}CoSiO{sub 4} and Li{sub 2}MnSiO{sub 4} were studied for the first time. • Both materials antiferromagnetically order around 12–14 K. • Despite different crystal structure magnetic structures are of the same type. • The fact is attributed to similar topology of magnetic interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Protein structure prediction guided by crosslinking restraints – A systematic evaluation of the impact of the crosslinking spacer length

Recent development of high-resolution mass spectrometry (MS) instruments enables chemical crosslinking (XL) to become a high-throughput method for obtaining structural information about proteins. Restraints derived from XL-MS experiments have been used successfully for structure refinement and protein–protein docking. However, one formidable question is under which circumstances XL-MS data might be sufficient to determine a protein’s tertiary structure de novo? Answering this question will not only include understanding the impact of XL-MS data on sampling and scoring within a de novo protein structure prediction algorithm, it must also determine an optimal crosslinker type and length for protein structure determination. While a longer crosslinker will yield more restraints, the value of each restraint for protein structure prediction decreases as the restraint is consistent with a larger conformational space. In this study, the number of crosslinks and their discriminative power was systematically analyzed in silico on a set of 2055 non-redundant protein folds considering Lys–Lys, Lys–Asp, Lys–Glu, Cys–Cys, and Arg–Arg reactive crosslinkers between 1 and 60 Å. Depending on the protein size a heuristic was developed that determines the optimal crosslinker length. Next, simulated restraints of variable length were used to de novo predict the tertiary structure of fifteen proteins using the BCL::Fold algorithm. The results demonstrate that a distinct crosslinker length exists for which information content for de novo protein structure prediction is maximized. The sampling accuracy improves on average by 1.0 Å and up to 2.2 Å in the most prominent example. XL-MS restraints enable consistently an improved selection of native-like models with an average enrichment of 2.1.

Biochemistry & Molecular Biology↗
DOE OSTI2016

Competing Pathways for Nucleation of the Double Perovskite Structure in the Epitaxial Synthesis of La 2 MnNiO 6

Over the past decades a confluence of advanced synthesis techniques, data-driven characterization, and rapid increases in computing power has sparked a renaissance in materials engineering. The emerging “materials-by-design” approach, while radically transforming the development of multicomponent systems, has tended to overlook the complex kinetic pathways that define materials synthesis. Although we are able to envision almost limitless materials combinations, we are unable to synthesize all of them in practice, since existing characterization and modeling approaches often fail to capture the inherent complexity of such systems. There is currently a disconnect between highly local structural characterization and macroscale properties measurements, resulting in oversimplified or incomplete structure-property models. Here we describe a multi-technique approach that combines aberration-corrected transmission electron microscopy with emerging oxide atom probe tomography to measure chemical ordering and extended defects in the model complex oxide, La2MnNiO6. We visualize cation ordering, as well as a three-dimensional network of secondary phases, which we describe in terms of ab initio structure calculations. We propose a defect model in which these phases alter their surrounding octahedral environment, severely disrupting cation superexchange. Through this array of experimental and theoretical techniques, we uncover fundamental structure-property relationships and illustrate a new approach to engineer complex, multicomponent systems.

atom probe tomography↗
DOE OSTI2016

Structure and Thermochemistry of Perrhenate Sodalite and Mixed Guest Perrhenate/Pertechnetate Sodalite

Treatment and immobilization of technetium-99 ( 99 Tc) contained in reprocessed nuclear waste and present in contaminated subsurface systems represents a major environmental challenge. One potential approach to managing this highly mobile and long-lived radionuclide is immobilization into micro- and meso-porous crystalline solids, specifically sodalite. We synthesized and characterized the structure of perrhenate sodalite, Na 8 [AlSiO 4 ]6(ReO 4 ) 2 , and the structure of a mixed guest perrhenate/pertechnetate sodalite, Na 8 [AlSiO 4 ] 6 (ReO 4 ) 2-x (TcO 4 ) x . Perrhenate was used as a chemical analogue for pertechnetate. Bulk analyses of each solid confirm a cubic sodalite-type structure (P$\overline{43}$n, No. 218 space group) with rhenium and technetium in the 7+ oxidation state. High-resolution nanometer scale characterization measurements provide first-of-a-kind evidence that the ReO 4 – anions are distributed in a periodic array in the sample, nanoscale clustering is not observed, and the ReO 4 – anion occupies the center of the sodalite β-cage in Na 8 [AlSiO 4 ] 6 (ReO 4 ) 2 . We also demonstrate, for the first time, that the TcO 4 – anion can be incorporated into the sodalite structure. Lastly, thermochemistry measurements for the perrhenate sodalite were used to estimate the thermochemistry of pertechnetate sodalite based on a relationship between ionic potential and the enthalpy and Gibbs free energy of formation for previously measured oxyanion-bearing feldspathoid phases. The results collected in this study suggest that micro- and mesoporous crystalline solids maybe viable candidates for the treatment and immobilization of 99 Tc present in reprocessed nuclear waste streams and contaminated subsurface environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

High-Pressure Structural Response of an Insensitive Energetic Crystal: Dihydroxylammonium 5,5'-Bistetrazole-1,1'-diolate (TKX-50)

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa. The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2 N 8 O 2 ) 2– ] linked with two cations [(NH 3 OH) + ] through four strong hydrogen bonds. The present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Sequence of Silicon Monolayer Structures Grown on a Ru Surface: from a Herringbone Structure to Silicene

Silicon-based two-dimensional (2D) materials are uniquely suited for integration in Si-based electronics. Silicene, an analogue of graphene, was recently fabricated on several substrates and was used to make a field-effect transistor. Here, we report that when Ru(0001) is used as a substrate, a range of distinct monolayer silicon structures forms, evolving toward silicene with increasing Si coverage. Low Si coverage produces a herringbone structure, a hitherto undiscovered 2D phase of silicon. With increasing Si coverage, herringbone elbows evolve into silicene-like honeycomb stripes under tension, resulting in a herringbone-honeycomb 2D superlattice. At even higher coverage, the honeycomb stripes widen and merge coherently to form silicene in registry with the substrate. Scanning tunneling microscopy (STM) was used to image the structures. The structural stability and electronic properties of the Si 2D structures, the interaction between the Si 2D structures and the Ru substrate, and the evolution of the distinct monolayer Si structures were elucidated by density functional theory (DFT) calculations. This work paves the way for further investigations of monolayer Si structures, the corresponding growth mechanisms, and possible functionalization by impurities.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Same Precursor, Two Different Products: Comparing the Structural Evolution of In–Ga–O “Gel-Derived” Powders and Solution-Cast Films Using Pair Distribution Function Analysis

Amorphous metal oxides are central to a variety of technological applications. In particular, indium gallium oxide has garnered attention as a thin-film transistor channel layer material. In this work we examine the structural evolution of indium gallium oxide gel-derived powders and thin films using infrared vibrational spectroscopy, X-ray diffraction, and pair distribution function (PDF) analysis of X-ray total scattering from standard and normal incidence thin-film geometries (tfPDF). We find that the gel-derived powders and films from the same aqueous precursor evolve differently with temperature, forming mixtures of Ga-substituted In2O3 and In-substituted β-Ga2O3 with different degrees of substitution. X-ray total scattering and PDF analysis indicate that the majority phase for both the powders and films is an amorphous/nanocrystalline β-Ga2O3 phase, with a minor constituent of In2O3 with significantly larger coherence lengths. This amorphous β-Ga2O3 phase could not be identified using the conventional Bragg diffraction techniques traditionally used to study crystalline metal oxide thin films. The combination of Bragg diffraction and tfPDF provides a much more complete description of film composition and structure, which can be used to detail the effect of processing conditions and structure–property relationships. This study also demonstrates how structural features of amorphous materials, traditionally difficult to characterize by standard diffraction, can be elucidated using tfPDF.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Stripe-like nanoscale structural phase separation in superconducting BaPb 1-x Bi x O 3

The phase diagram of BaPb 1-x Bi x O 3 exhibits a superconducting dome in the proximity of a charge density wave phase. For the superconducting compositions, the material coexists as two structural polymorphs. Here we show, via high-resolution transmission electron microscopy, that the structural dimorphism is accommodated in the form of partially disordered nanoscale stripes. Identification of the morphology of the nanoscale structural phase separation enables determination of the associated length scales, which we compare with the Ginzburg–Landau coherence length. We find that the maximum T c occurs when the superconducting coherence length matches the width of the partially disordered stripes, implying a connection between the structural phase separation and the shape of the superconducting dome.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗