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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The seventh blind test of crystal structure prediction: structure generation methods

A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.

Chemistry↗
DOE OSTI2019

Structural analysis of Gd 6 FeBi 2 from single-crystal X-ray diffraction methods and electronic structure calculations

The crystal structure of the gadolinium iron bis­muthide Gd 6 FeBi 2 has been characterized by single-crystal X-ray diffraction data and analyzed in detail using first-principles calculations. The structure is isotypic with the Zr 6 CoAl 2 structure, which is a variant of the ZrNiAl structure and its binary prototype Fe 2 P (Pearson code hP 9, Wyckoff sequence g f d a ). As such, the structure is best viewed as an array of tricapped trigonal prisms of Gd atoms centered alternately by Fe and Bi. The magnetic-ordering temperature of this compound ( ca 350 K) is much higher than that of other rare-earth metal-rich phases with the same or related structures. It is also higher than the ordering temperature of many other Gd-rich ternary phases, where the magnetic exchange is typically governed by Ruderman–Kittel–Kasuya–Yosida (RKKY) inter­actions. First-principles calculations reveal a larger than expected Gd magnetic moment, with the additional contribution arising from the Gd 5 d electrons. The electronic structure analysis suggests strong Gd 5 d –Fe 3 d hybridization to be the cause of this effect, rather than weak inter­actions between Gd and Bi. These details are of importance for understanding the magnetic response and explaining the high ordering tem­per­ature in this material.

Chemistry↗
DOE OSTI2015

Structure of the HIV-1 reverse transcriptase Q151M mutant: insights into the inhibitor resistance of HIV-1 reverse transcriptase and the structure of the nucleotide-binding pocket of Hepatitis B virus polymerase

The structure of the HIV-1 reverse transcriptase Q151M mutant was determined at a resolution of 2.6 Å in space group P321. Hepatitis B virus polymerase (HBV Pol) is an important target for anti-HBV drug development; however, its low solubility and stability in vitro has hindered detailed structural studies. Certain nucleotide reverse transcriptase (RT) inhibitors (NRTIs) such as tenofovir and lamivudine can inhibit both HBV Pol and Human immunodeficiency virus 1 (HIV-1) RT, leading to speculation on structural and mechanistic analogies between the deoxynucleotide triphosphate (dNTP)-binding sites of these enzymes. The Q151M mutation in HIV-1 RT, located at the dNTP-binding site, confers resistance to various NRTIs, while maintaining sensitivity to tenofovir and lamivudine. The residue corresponding to Gln151 is strictly conserved as a methionine in HBV Pol. Therefore, the structure of the dNTP-binding pocket of the HIV-1 RT Q151M mutant may reflect that of HBV Pol. Here, the crystal structure of HIV-1 RT Q151M, determined at 2.6 Å resolution, in a new crystal form with space group P321 is presented. Although the structure of HIV-1 RT Q151M superimposes well onto that of HIV-1 RT in a closed conformation, a slight movement of the β-strands (β2–β3) that partially create the dNTP-binding pocket was observed. This movement might be caused by the introduction of the bulky thioether group of Met151. The structure also highlighted the possibility that the hydrogen-bonding network among amino acids and NRTIs is rearranged by the Q151M mutation, leading to a difference in the affinity of NRTIs for HIV-1 RT and HBV Pol.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Structural health monitoring of engineered structures using a space-borne synthetic aperture radar multi-temporal approach: from cultural heritage sites to war zones

Typically, structural health monitoring (SHM) of engineered structures consists of an automated or semi-automated survey system that seeks to assess the structural condition of an anthropogenic structure. The aim of an SHM system is to provide insights into possible induced damage or any inherent signals of deformation affecting the structure in terms of detection, localization, assessment, and prediction. During the last decade there has been a growing interest in using several remote sensing techniques, such as synthetic aperture radar (SAR), for SHM. Constellations of SAR satellites with short repeat time acquisitions permit detailed surveys temporal resolution and millimetric sensitivity to deformation that are at the scales relevant to monitoring large structures. The all-weather multi-temporal characteristics of SAR make its products suitable for SHM systems, especially in areas where in situ measurements are not feasible or not cost effective. To illustrate this capability, we present results from COSMO-SkyMed (CSK) and TerraSAR-X SAR observations applied to the remote sensing of engineered structures. We show how by using multiple-geometry SAR-based products which exploit both phase and amplitude of the SAR signal we can address the main objectives of an SHM system including detection and localization. We highlight that, when external data such as rain or temperature records are available or simple elastic models can be assumed, the SAR-based SHM capability can also provide an interpretation in terms of assessment and prediction. We highlight examples of the potential for such imaging capabilities to enable advances in SHM from space, focusing on dams and cultural heritage areas.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

In Situ ATR-FTIR Study of the Cathode–Electrolyte Interphase: Electrolyte Solution Structure, Transition Metal Redox, and Surface Layer Evolution

We present a study of the lithium nickel manganese cobalt oxide (LiNi 0.6 Mn 0.2 Co 0.2 O 2 , NMC622) cathode-electrolyte interphase (CEI) during galvanostatic charging and discharging using in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) methods to investigate the voltage dependent electrolyte solution structure changes at the interface, transition metal (TM) redox chemistry, and cathode/electrolyte interfacial layer evolution. Furthermore, our in situ cell design provides both reliable electrochemical device testing and strong FTIR vibrational absorption signals near the cathode surface. Specifically, advanced spectral analysis elucidates changes of near-surface Li+ ion (de)solvation by solvent molecules during galvanostatic cycling. Moreover, cathode metal-oxygen vibrational absorptions, sensitive to TM redox behaviors and subsequent local structural variations, were correlated to cathode de-lithiation (and lithiation) and electrolyte solution structure changes. In addition, we have detected the formation and evolution of a CEI surface layer on the NMC622 cathode that contributes to the cell's capacity fade.

25 ENERGY STORAGE↗
DOE OSTI2026

Improved Accuracy in Semi-Experimental Structure Determination by Resolving Problems Associated with Rotation of Principal Inertial Axes of Isotopologues: Structures of 1,3-Oxazole ( c -C 3 H 3 NO)

The rotational spectrum of the normal isotopologue of 1,3-oxazole (c-C 3 H 3 NO) was observed from 43 to 750 GHz. Over 3900 transitions for the ground vibrational state are measured, assigned, and least-squares fit to sextic centrifugally distorted-rotor Hamiltonians. The measured frequencies and resulting spectroscopic constants from this extended spectral range, combined with previous measurements of the nuclear quadrupole coupling constants, will facilitate astronomical searches for oxazole across the majority of the range of modern radiotelescopes. Spectra for a set of 30 oxazole isotopologues, which include multiple isotopic substitutions of each atom, are used to determine the first semi-experimental equilibrium ($r$$^{SE}_{e}$) structure and semi-experimental substitution structure ($r$$^{SE}_{e}$), each using CCSD(T) computed values for the vibration–rotation interaction and electron-mass corrections. The large number of isotopologues, including 21 isotopologues observed for the first time, and the redundant substitutions of each atom provide sufficient spectroscopic information to determine the $r$$^{SE}_{e}$ structure with the expected high level of accuracy and precision (0.0001 or 0.0002 Å in bond distances and 0.013 to 0.025° in bond angles). In the course of this study, we analyzed a known issue for some $r$$^{SE}_{e}$ structure determinations of near-oblate asymmetric tops in which inclusion of individual isotopologues degrades the structure determination. We demonstrate that this problem primarily arises from the difference in the values of the computed vibration–rotation interaction corrections as evaluated at the computed re geometry vs the $r$$^{SE}_{e}$ geometry of the “real” molecule. Our solution to this problem substantially improves the $r$$^{SE}_{e}$ structure of oxazole and likely can be generalized to many other molecules.

Chemical structure↗
DOE OSTI2015

Probing microhydration effect on the electronic structure of the GFP chromophore anion: Photoelectron spectroscopy and theoretical investigations

The photophysics of the Green Fluorescent Protein (GFP) chromophore is critically dependent on its local structure and on its environment. Despite extensive experimental and computational studies, there remain many open questions regarding the key fundamental variables that govern this process. One outstanding problem is the role of autoionization as a possible relaxation pathway of the excited state under different environmental conditions. This issue is considered in our work through combined experimental and theoretical studies of microsolvated clusters of the deprotonated p-hydroxybenzylidene-2,3-dimethylimidazolinone anion (HBDI{sup −}), an analog of the GFP chromophore. Through selective generation of microsolvated structures of predetermined size and subsequent analysis of experimental photoelectron spectra by high level ab initio methods, we are able to precisely identify the structure of the system, establish the accuracy of theoretical data, and provide reliable description of auto-ionization process as a function of hydrogen-bonding environment. Our study clearly illustrates the first few water molecules progressively stabilize the excited state of the chromophore anion against the autodetached neutral state, which should be an important trait for crystallographic water molecules in GFPs that has not been fully explored to date.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Density functional study of the electronic structure of dye-functionalized fullerenes and their model donor-acceptor complexes containing P3HT

We study the electronic structure of C{sub 60} fullerenes functionalized with a thiophene-diketo-pyrrolopyrrole-thiophene based chromophore using density functional theory combined with large polarized basis sets. As the attached chromophore has electron donor character, the functionalization of the fullerene leads to a donor-acceptor (DA) system. We examine in detail the effect of the linker and the addition site on the electronic structure of the functionalized fullerenes. We further study the electronic structure of these DA complexes with a focus on the charge transfer excitations. Finally, we examine the interface of the functionalized fullerenes with the widely used poly(3-hexylthiophene-2,5-diyl) (P3HT) donor. Our results show that all functionalized fullerenes with an exception of the C{sub 60}-pyrrolidine [6,6], where the pyrrolidine is attached at a [6,6] site, have larger electron affinities relative to the pristine C{sub 60} fullerene. We also estimate the quasi-particle gap, lowest charge transfer excitation energy, and the exciton binding energies of the functionalized fullerene-P3MT model systems. Results show that the exciton binding energies in these model complexes are slightly smaller compared to a similarly prepared phenyl-C{sub 61}-butyric acid methyl ester (PCBM)-P3MT complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Structural stability, electronic structure and mechanical properties of alkali gallium hydrides AGaH{sub 4} (A = Li, Na)

Ab initio calculations are performed to investigate the structural stability, electronic structure and mechanical properties of alkali gallium hydrides AGaH{sub 4} (A = Li, Na) for three different crystal structures, namely tetragonal (P42{sub 1}c), tetragonal (P4{sub 2}/nmc) and monoclinic (P2{sub 1}/c). Among the considered structures, tetragonal (P42{sub 1}c) phase is found to be the most stable phase for these hydrides at normal pressure. A pressure induced structural phase transition from tetragonal (P42{sub 1}c) to tetragonal (P4{sub 2}/nmc) is observed. The electronic structure reveals that these hydrides are insulators. The calculated elastic constants indicate that these ternary imides are mechanically stable at normal pressure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Surrogate Hessian accelerated structural optimization for stochastic electronic structure theories

In this work, we present an efficient energy-based method for structural optimization with stochastic electronic structure theories, such as diffusion quantum Monte Carlo (DMC). This method is based on robust line-search energy minimization in reduced parameter space, exploiting approximate but accurate Hessian information from a surrogate theory, such as density functional theory. The surrogate theory is also used to characterize the potential energy surface, allowing for simple but reliable ways to maximize statistical efficiency while retaining controllable accuracy. We demonstrate the method by finding the minimum DMC energy structures of the selected flake-like aromatic molecules, such as benzene, coronene, and ovalene, represented by 2, 6, and 19 structural parameters, respectively. In each case, the energy minimum is found within two parallel line-search iterations. The method is near-optimal for a line-search technique and suitable for a broad range of applications. It is easily generalized to any electronic structure method where forces and stresses are still under active development and implementation, such as diffusion Monte Carlo, auxiliary-field Monte Carlo, and stochastic configuration interaction, as well as deterministic approaches such as the random-phase approximation. Accurate and efficient means of geometry optimization could shed light on a broad class of materials and molecules, showing high sensitivity of induced properties to structural variables.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structural motifs and bonding in two families of boron structures predicted at megabar pressures

The complex crystal chemistry of elemental boron has led to numerous proposed structures with distinctive motifs as well as contradictory findings. Herein, evolutionary structure searches performed at 100 GPa have uncovered a series of metastable phases of boron, and bonding analyses were carried out to elucidate their electronic structure. These polymorphs, dynamically stable at 100 GPa, were grouped into two families. Here, the first was derived from the thermodynamic minimum at these conditions, α-Ga, whereas channels comprised the second. Two additional intergrowth structures were uncovered, and it was shown they could be constructed by stacking layers of α-Ga-like and channel-like allotropes on top of each other. A detailed bonding analysis revealed networks of four-center σ-bonding functions linked by two-center B-B bonds in the α-Ga based structures, and networks that were largely composed of three-center σ-bonding functions in the channel-based structures. Seven of these high-pressure phases were found to be metastable at atmospheric conditions, and their Vickers hardnesses were estimated to ≈ 36 GPa.

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

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Insight into the structural ambiguity of actinide(IV) oxalate sheet structures: a case for alternate coordination geometries

Plutonium(IV) oxalate hexahydrate (Pu(C 2 O 4 ) 2 ∙ 6H 2 O; PuOx) is an important intermediate in the recovery of plutonium from used nuclear fuel. Its formation via precipitation is well studied, yet its crystal structure remains unknown. Instead, the crystal structure of PuOx is assumed to be isostructural with neptunium(IV) oxalate hexahydrate (Np(C 2 O 4 )­ 2 ∙ 6H 2 O; NpOx) and uranium(IV) oxalate hexahydrate (U(C 2 O 4 )­ 2 ∙ 6H 2 O; UOx) despite the high degree of unresolved disorder that exists when determining water positions in the crystal structures of the latter two compounds. Such assumptions regarding the isostructural behavior of the actinide elements have been used to predict the structure of PuOx for use in a wide range of studies. Herein, we report the first crystal structures for PuOx and Th(C 2 O 4 ) 2 · 6H 2 O (ThOx). This data, along with new characterization of UOx and NpOx, has resulted in the full determination of the structures and resolution of the disorder around the water molecules. Specifically, we identify the coordination of two water molecules with each metal center, which necessitates a change in oxalate coordination mode from axial to equatorial that has not been reported in the literature. Here this work exemplifies the need to revisit previous assumptions regarding fundamental actinide chemistry, which are heavily relied upon within the current nuclear field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Structural complexity of γ-Al 2 O 3 : The nature of vacancy ordering and the structure of complex antiphase boundaries

The structure of γ-Al2O3 remains largely undetermined despite decades of research. This is due to the high degree of disorder, which poses significant challenges for structural analysis using conventional crystallographic approaches. Herein, we study the structure of γ-Al2O3 with Scanning Transmission Electron Microscopy (STEM) and ab-initio calculations to provide a complete structural description. We show that the microstructure can be understood in terms of two key structural features of nanoscale spinel domains and finite thickness segments termed as complex antiphase boundaries (cAPB) that provide the domain interconnectivity. The spinel domains have a distinctive preference for vacancy ordering, which can be rationalized in terms of a structure with a stacking disorder. Tetragonal P4 1 2 1 2 or monoclinic P2 1 models, all based on the identical motif, can be considered as representative ordered forms. Individual spinel domains are interconnected via cAPBs, which adopt a distinct non-spinel bonding environment of δ-Al 2 O 3 . The most common cAPB consists of a single delta motif with thickness of just 0.6 nm on (001), with the resulting displacement a/4 [101]. Remarkably, the cAPBs are shown to energetically stabilize the spinel domains of γ-Al 2 O 3 explaining their high abundance. We demonstrate how the tetragonal distortions naturally arise in this intricate microstructure and place the proposed model in the context of phase transformations to high temperature transition aluminas.

36 MATERIALS SCIENCE↗