Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Crystal structure prediction”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Role of Short-Range Order on Diffusion Coefficients in the Li–Mg Alloy

Li–Mg alloys are important because of their beneficial role in fostering uniform plating and stripping of lithium in all-solid-state batteries. The alloy Li x Mg 1–x forms a solid solution on the BCC crystal structure when the lithium content is greater than x ≈ 0.3. The activation barriers of lithium and magnesium exchanges with a vacancy, crucial for substitutional diffusion, are predicted to be exceptionally low and almost identical, with negligible dependence on the alloy composition. The equilibrium vacancy concentration at room temperature is predicted to be very low, and it also remains almost constant with no dependence on Mg content in the alloy (for x Li ≥ 0.5). Nevertheless, both experiments and kinetic Monte Carlo simulations indicate that the tracer diffusion coefficients decrease by almost an order of magnitude with the addition of Mg to the alloy. In this contribution, the crucial role that chemical short-range order plays in affecting the diffusion coefficients is studied. Chemical short-range order is found to increase the effective activation barrier for lithium and magnesium diffusion by making successive atomic hops with vacancies correlated.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Development of Porous Crystalline Materials for Selective Binding of O 2 from Air

Porous materials that take advantage of different chemisorptive behaviors of O 2 and N 2 could be an effective alternative to approaches based on physisorption for this important separation. Recently, the tetra-nuclear cobalt complex [(Co(III) 2 (bpbp)O 2 ) 2 bdc](PF 6 ) 4 (CSD code: GAMVIB; bpbp – = 2,6-bis(N,N-bis(2-pyridylmethyl)aminomethyl)-4-tert-butylphenolato; bdc 2– = 1,4-benzenedicarboxylato) was shown to have potential for O 2 /N 2 separations based on this concept. This observation raises the question of what other known materials have similar properties. Here, we combine structure screening with a high-throughput periodic density functional theory (DFT) workflow to investigate O 2 and N 2 adsorption in materials from validated crystal structure databases (e.g., CoRE-MOF database and CSD database). These calculations identify multiple materials that have similar di-Co clusters to GAMVIB that are predicted to selectively bind O 2 over N 2 , and suggest design rules that can be used to tune the O 2 and N 2 affinities in materials of this kind.

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

Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication

Abstract Mosquito-borne flaviviruses (MBFVs) including dengue, West Nile, yellow fever, and Zika viruses have an RNA genome encoding one open reading frame flanked by 5′ and 3′ untranslated regions (UTRs). The 3′ UTRs of MBFVs contain regions of high sequence conservation in structured RNA elements known as dumbbells (DBs). DBs regulate translation and replication of the viral RNA genome, functions proposed to depend on the formation of an RNA pseudoknot. To understand how DB structure provides this function, we solved the x-ray crystal structure of the Donggang virus DB to 2.1Å resolution and used structural modeling to reveal the details of its three-dimensional fold. The structure confirmed the predicted pseudoknot and molecular modeling revealed how conserved sequences form a four-way junction that appears to stabilize the pseudoknot. Single-molecule FRET suggests that the DB pseudoknot is a stable element that can regulate the switch between translation and replication during the viral lifecycle by modulating long-range RNA conformational changes.

Akiyama, Benjamin M.↗
DOE OSTI2021

Thermal conductivity of CaSiO 3 perovskite at lower mantle conditions

Thermal conductivity (κ) of mantle minerals is key to understanding dynamics in the deep Earth. It controls the style of mantle convection and the timescale of cooling both the mantle and the core. Cubic CaSiO 3 perovskite (CaPv) is the third most abundant mineral in the lower mantle (7 vol %). Despite its importance, no theoretical or experimental estimate of CaPv's κ is available. Theoretical investigations of its properties are challenging because of its strong anharmonicity. Experimental measurements at relevant pressures and temperatures are equally challenging. Here we present ab initio results for CaPv's κ obtained using the phonon quasiparticle approach to address its strong anharmonicity. We also offer experimental measurements of κ up to 67 GPa and 1950 K. Predictions and measurements are in good agreement and reveal a surprisingly large κ for cubic CaPv that can be explained on the basis of its high crystal structure symmetry. Despite its relatively low abundance, CaPv's κ increases the lower mantle κ by ~10 %, if accounted for. κ of mantle regions enriched in subducted crustal materials will be more strongly impacted.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Spin dynamics of the centrosymmetric skyrmion material GdRu 2 Si 2

Magnetic skyrmion crystals are traditionally associated with non-centrosymmetric crystal structures; however, it has been demonstrated that skyrmion crystals can be stabilized by competing interactions in centrosymmetric crystals. To understand and optimize the physical responses associated with topologically nontrivial skyrmion textures, it is important to quantify their magnetic interactions by comparing theoretical predictions with spectroscopy data. Here, we present neutron diffraction and spectroscopy data on the centrosymmetric skyrmion material GdRu 2 Si 2 and show that the key spectroscopic features can be explained by magnetic interactions calculated using density functional theory. We further show that the recently proposed 2-q “topological spin stripe” structure yields better agreement with our data than a 1-q helical structure and identify how the magnetic structure evolves with temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Crystal chemistry at high pressure

The chemistry we are taught in school, and we experience in our daily existence occurs at 1 atm. However, pressure spans an astounding 62 orders of magnitude in the Universe in going from the void of interstellar space to the crushing conditions at the center of a neutron star. The way in which pressure affects chemistry is important for Earth and planetary sciences, materials science, in understanding the extreme conditions experienced in nuclear explosions, and it may be key in addressing the future energy needs of our society. In this article we outline how the often neglected pressure variable affects chemistry, beginning from the way in which atomic energy levels are altered. This lays the foundation for understanding the unique crystal and electronic structures that emerge when matter is squeezed, as well as pressure’s effect on chemical reactivity. Finally, we give an overview of the main concepts behind conventional, or phonon-mediated, superconductivity, and describe how the pressure variable may be key in discovering and designing light-element based materials whose superconducting critical temperatures approach room temperature. Here, we discuss some of the main families of superconducting hydrides that have been predicted computationally, and the experimental successes in this exciting and rapidly developing field.

Chemical bonding↗
DOE OSTI2020

Structural Tolerance Factor Approach to Defect-Resistant I 2 -II-IV-X 4 Semiconductor Design

Recent work on quaternary semiconductors Cu 2 BaSn(S,Se) 4 and Ag 2 BaSnSe 4 for photovoltaic and thermoelectric applications, respectively, has shown the promise of exploring the broader family of defect-resistant I 2 -II-IV-X 4 materials (where I, II, and IV refer to the formal oxidation state of the metal cations and X is a chalcogen anion) with tetrahedrally coordinated I/IV cations and larger II cations (i.e., Sr, Ba, Pb, and Eu) for optoelectronic and energy-related applications. Chemical dissimilarity among the II and I/IV atoms represents an important design motivation because it presents a barrier to antisite formation, which otherwise may act as electronically harmful defects. We herein show how all 31 experimentally reported I 2 -II-IV-X 4 examples (with large II cations and tetrahedrally coordinated smaller I/IV cations), which form within five crystal structure types, are structurally linked. Based on these structural similarities, we derive a set of tolerance factors that serve as descriptors for phase stability within this family. Despite common usage in the well-studied perovskite system, Shannon ionic radii are found to be insufficient for predicting metal–chalcogen bond lengths, pointing to the need for experimentally derived correction factors as part of an empirically driven learning approach to structure prediction. Here, we use the tolerance factors as a predictive tool and demonstrate that four new I 2 -II-IV-X 4 compounds, Ag 2 BaSiS 4 , Ag 2 PbSiS 4 , Cu 2 PbGeS 4 , and Cu 2 SrSiS 4 , can be synthesized in correctly predicted phases. One of these compounds, Ag 2 PbSiS 4 , shows potentially promising optoelectronic properties for photovoltaic applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Phase stability in the Hf-N and Zr-N systems

Hf and Zr nitrides are promising compounds for many technologically important areas, including high-temperature structural applications, quantum computing, and solar and optical applications. Here, this article reports on a comprehensive first-principles statistical mechanics study of phase stability in the Hf-N and Zr-N binary systems. A high solubility of nitrogen in the hcp forms of Hf and Zr is predicted. The rocksalt forms of HfN and ZrN can also tolerate a high degree of off-stoichiometry through the introduction of nitrogen and metal vacancies. The Hf-N binary favors a family of stacking faulted parent crystal structures at intermediate nitrogen concentrations that host a unique form of short-range order among nitrogen interstitials and vacancies. These phases can accommodate some degree of configurational entropy and remain ordered to temperatures as high as 1200 K.

Monte Carlo methods↗
DOE OSTI2026

Leveraging the redox activities of cerium and dibenzotetrathiafulvalene to discover a photo-responsive magnetic material

Stimuli-responsive changes in lanthanide-based materials are a promising research direction. In this study, [DBTTF] 4 [Ce 2 Cl 10 ] DBTTF = dibenzotetrathiafulvalene (1) was synthesized by a light-induced crystallization, where photo-oxidation of DBTTF enables formation of the cerium dimer [Ce 2 Cl 10 ] 4− . Intermolecular interactions between the stacked organic units of the crystal result in charge transfer bands in the visible-NIR (near-infrared) region, evident in the solid-state absorption spectrum upon comparison with the solution spectrum. The assignments of the sublattice oxidation states were made with single-crystal X-ray diffraction (SC-XRD) structural characterization, Raman spectroscopy, X-ray absorption spectroscopy, and magnetometry. Continuous 532 nm laser irradiation of the microcrystalline solid modulates the redox states in 1, leading to ∼40% reduction in the observed magnetization at 2 K. Density functional theory PBE+U/HSE06 band structure calculations predict Mott insulating behavior in 1, with a bandgap of 0.54/0.81 eV, and further support the conjecture that the observed photo-induced change in magnetization results from electron transfer from the [Ce 2 Cl 10 ] 4− anions to the π-stacked [DBTTF] 2 2+ organic dimer subunits. An enhancement in conductivity is similarly observed upon 532 nm irradiation, determined by single-crystal transport measurements. The findings reveal that photo-responsive lanthanide-based materials can be achieved by integration of redox-active organic moieties with redox-active lanthanide cations for the realization of switchable, photo-magnetic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

The structural information filtered features (SIFF) potential: Maximizing information stored in machine-learning descriptors for materials prediction

Machine learning inspired potentials continue to improve the ability for predicting structures of materials. However, many challenges still exist, particularly when calculating structures of disordered systems. These challenges are primarily due to the rapidly increasing dimensionality of the feature-vector space which in most machine-learning algorithms is dependent on the size of the structure. In this article, we present a feature-engineered approach that establishes a set of principles for representing potentials of physical structures (crystals, molecules, and clusters) in a feature space rather than a physically motivated space. Our goal in this work is to define guiding principles that optimize information storage of the physical parameters within the feature representations. In this manner, we focus on keeping the dimensionality of the feature space independent of the number of atoms in the structure. Our Structural Information Filtered Features (SIFF) potential represents structures by utilizing a feature vector of low-correlated descriptors, which correspondingly maximizes information within the descriptor. We present results of our SIFF potential on datasets composed of disordered (carbon and carbon–oxygen) clusters, molecules with C 7 O 2 H 2 stoichiometry in the GDB9-14B dataset, and crystal structures of the form (Al x Ga y In z ) 2 O 3 as proposed in the NOMAD Kaggle competition. Our potential's performance is at least comparable, sometimes significantly more accurate, and often more efficient than other well-known machine-learning potentials for structure prediction. However, primarily, we offer a different perspective on how researchers should consider opportunities in maximizing information storage for features.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Engineering Supramolecular Hybrid Architectures with Directional Organofluorine Bonds

Understanding how chemical modifications alter the atomic‐scale organization of materials is of fundamental importance in materials engineering and the target of considerable efforts in computational prediction. Incorporating covalent and noncovalent interactions in designing crystals while “piggybacking” on the driving force of molecular self‐assembly has augmented efforts to understand the emergence of complex structures using directed synthesis. In this work, microcrystalline powders of the silver 2‐, 3‐, and 4‐fluorobenzenethiolates are prepared and their structures are resolved by small‐molecule serial femtosecond X‐ray crystallography. These three compounds enable the emergence and role of supramolecular synthons in the crystal structures of 3D metal‐organic chalcogenolates to be examined. The unique divergence in their optoelectronic, morphological, and structural behaviors is assessed. The extent of CHF interactions and their influence on the structure and the observed trends in the thermal stability of the crystals are quantified through theoretical calculations and thermogravimetric analysis.

Kotei, Patience A.↗
DOE OSTI2024

Cryo-EM Structure of the Mnx Protein Complex Reveals a Tunnel Framework for the Mechanism of Manganese Biomineralization

The global manganese cycle relies on microbes to oxidize soluble Mn(II) to insoluble Mn(IV) oxides. Some microbes require peroxide or superoxide as oxidants, but others can use O 2 directly, via multicopper oxidase (MCO) enzymes. One of these, MnxG from Bacillus sp. strain PL-12, was isolated in tight association with small accessory proteins, MnxE and MnxF. The protein complex, called Mnx, has eluded crystallization efforts, but we now report the 3D structure of a point mutant using cryo-EM single particle analysis, cross-linking mass spectrometry, and AlphaFold Multimer prediction. The ß-sheet–rich complex features MnxG enzyme, capped by a heterohexameric ring of alternating MnxE and MnxF subunits, and a tunnel that runs through MnxG and its MnxE 3 F 3 cap. The tunnel dimensions and charges can accommodate the mechanistically inferred binuclear manganese intermediates. Furthermore, comparison with the Fe(II)-oxidizing MCO, ceruloplasmin, identifies likely coordinating groups for the Mn(II) substrate, at the entrance to the tunnel. Thus, the 3D structure provides a rationale for the established manganese oxidase mechanism, and a platform for further experiments to elucidate mechanistic details of manganese biomineralization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Discovery of GuaB inhibitors with efficacy against Acinetobacter baumannii infection

ABSTRACT Guanine nucleotides are required for growth and viability of cells due to their structural role in DNA and RNA, and their regulatory roles in translation, signal transduction, and cell division. The natural antibiotic mycophenolic acid (MPA) targets the rate-limiting step inde novoguanine nucleotide biosynthesis executed by inosine-5´-monophosphate dehydrogenase (IMPDH). MPA is used clinically as an immunosuppressant, but whetherin vivoinhibition of bacterial IMPDH (GuaB) is a valid antibacterial strategy is controversial. Here, we describe the discovery of extremely potent small molecule GuaB inhibitors (GuaBi) specific to pathogenic bacteria with a low frequency of on-target spontaneous resistance and bactericidal efficacyin vivoagainstAcinetobacter baumanniimouse models of infection. The spectrum of GuaBi activity includes multidrug-resistant pathogens that are a critical priority of new antibiotic development. Co-crystal structures ofA. baumannii, Staphylococcus aureus, andEscherichia coliGuaB proteins bound to inhibitors show comparable binding modes of GuaBi across species and identifies key binding site residues that are predictive of whole-cell activity across both Gram-positive and Gram-negative clades of Bacteria. The clearin vivoefficacy of these small molecule GuaB inhibitors in a model ofA. baumanniiinfection validates GuaB as an essential antibiotic target. IMPORTANCE The emergence of multidrug-resistant bacteria worldwide has renewed interest in discovering antibiotics with novel mechanism of action. For the first time ever, we demonstrate that pharmacological inhibition ofde novoguanine biosynthesis is bactericidal in a mouse model ofAcinetobacter baumanniiinfection. Structural analyses of novel inhibitors explain differences in biochemical and whole-cell activity across bacterial clades and underscore why this discovery may have broad translational impact on treatment of the most recalcitrant bacterial infections.

Microbiology↗
DOE OSTI2023

Atomic-scale cryogenic electron microscopy imaging of self-assembled peptoid nanostructures

Amphiphilic polypeptoids with defined sequences, versatile in forming various nanostructures, are ideal for mimicking biomacromolecular structures. The predictive design of nanostructures depends on our understanding of the relationship between molecular structure and the locations of atoms in the nanostructure. Factors of importance include chain conformation, crystal motifs, and the arrangement of the molecules within the nanostructure. Here, this review introduces the cryogenic transmission electron microscopy (cryo-TEM) method, sorting and averaging unit cells in nanosheets for resolution enhancement and identifying structural heterogeneity. The resulting atomic-scale images reveal the presence of two types of crystal motifs. The impact of processing conditions, capping group chemistry, and side chain chemistry on structural heterogeneity and crystal motifs can be quantified. The 3D reconstruction of nanosheets, wherein atomic-scale corrugations were revealed, is introduced in this review. New developments in cryo-TEM, such as phase retrieval reconstruction, hold great promise for atomic-scale imaging of soft nanostructures.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Handbook on the Material Properties of Yttrium Hydride for High Temperature Moderator Applications

Yttrium hydride is an optimal choice for a high-temperature moderator material in advanced thermal neutron spectrum reactors that require small core volumes. A complete database of the thermomechanical properties of yttrium hydride is not yet available, although it is much needed to understand and predict the moderator performance during service in reactors. This milestone report presents the properties of unirradiated bulk yttrium hydride as a function of hydrogen concentration—including density, crystal structure, specific heat capacity, thermal diffusivity, thermal conductivity, hardness, elastic/shear moduli, Poisson’s ratio, fracture strength, microstructure, and thermal stability. This information provides a baseline measurement for the subsequent neutron irradiation response study of yttrium hydride. The recommended empirical treatment of the data is suggested. In addition, other properties (i.e., hydrogen retention, thermal hydrogen migration, and irradiation response) requiring investigation are discussed. Also included are the Preliminary post-irradiation examination (PIE) data of yttrium hydride irradiated at 600 and 900°C to 0.1 dpa in the High Flux Isotope Reactor (HFIR). The thermophysical properties have insignificant change following this low dpa irradiation for both irradiation temperatures.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Conditions of coherent-phonon excitation in SrMnSb2 films and crystals

Excitation of coherent phonons has the potential to dramatically alter the electronic structure of Dirac and Weyl semimetals, enabling sub-picosecond control of their optical and electronic properties. The Dirac semimetal SrMnSb2 is a candidate for such control, with a coherent-phonon mode that is predicted to close and reopen a gap at the Dirac node. Here, through a series of ultrafast pump-probe experiments, we establish suitable samples and conditions for driving the coherent phonon to high amplitude and attempting to observe the gap’s closure. Films of SrMnSb2 grown by molecular-beam epitaxy are shown to have phononic properties matching those of bulk crystals. We find that the phonon can be strongly excited by pump pulses with wavelength near 1500 nm, which will excite a 30-nm film almost uniformly and will penetrate the arsenic capping layers that protect the films. We find that samples withstand pump pulses of fluence up to 20 mJ/cm2, and we demonstrate the potential for sequences of pulses to amplify the oscillation while suppressing other phonon modes. Armed with our new knowledge of the conditions for exciting the desired coherent phonon, future experiments will be well prepared to measure its motion and to observe phononic control of the Dirac-point gap.

Rai, Manita↗
DOE OSTI2024

Molecular Mechanisms of Sorbed Ion Effects during Boehmite Particle Aggregation

Classical theories of particle aggregation, such as Derjaguin–Landau–Verwey–Overbeek (DLVO), do not explain recent observations of ion-specific effects or the complex concentration dependence for aggregation. Thus, here, we probe the molecular mechanisms by which selected alkali nitrate ions (Na + , K + , and NO 3 –) influence aggregation of the mineral boehmite (γ-AlOOH) nanoparticles. Nanoparticle aggregation was analyzed using classical molecular dynamics (CMD) simulations coupled with the metadynamics rare event approach for stoichiometric surface terminations of two boehmite crystal faces. Calculated free energy landscapes reveal how electrolyte ions alter aggregation on different crystal faces relative to pure water. Consistent with experimental observations, we find that adding an electrolyte significantly reduces the energy barrier for particle aggregation (~3–4×). However, in this work, we show this is due to the ions disrupting interstitial water networks, and that aggregation between stoichiometric (010) basal–basal surfaces is more favorable than between (001) edge–edge surfaces (~5–6×) due to the higher interfacial water densities on edge surfaces. The interfacial distances in the interlayer between aggregated particles with electrolytes (~5–10 Å) are larger than those in pure water (a few Ångströms). Together, aggregation/disaggregation in salt solutions is predicted to be more reversible due to these lower energy barriers, but there is uncertainty on the magnitudes of the energies that lead to aggregation at the molecular scale. By analyzing the peak water densities of the first monolayer of interstitial water as a proxy for solvent ordering, we find that the extent of solvent ordering likely determines the structures of aggregated states as well as the energy barriers to move between them. Further, the results suggest a path for developing a molecular-level basis to predict the synergies between ions and crystal faces that facilitate aggregation under given solution conditions. Such fundamental understanding could be applied extensively to the aggregation and precipitation utilization in the biological, pharmaceutical, materials design, environmental remediation, and geological regimes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Structure Prediction of Ionic Epitaxial Interfaces with Ogre Demonstrated for Colloidal Heterostructures of Lead Halide Perovskites

Colloidal epitaxial heterostructures are nanoparticles composed of two different materials connected at an interface, which can exhibit properties different from those of their individual components. Combining dissimilar materials offers exciting opportunities to create a wide variety of functional heterostructures. However, assessing structural compatibility–the main prerequisite for epitaxial growth–is challenging when pairing complex materials with different lattice parameters and crystal structures. This complicates both the selection of target heterostructures for synthesis and the assignment of interface models when new heterostructures are obtained. Here, we demonstrate Ogre as a powerful tool to accelerate the design and characterization of colloidal heterostructures. To this end, we implemented developments tailored for the high-efficiency prediction of epitaxial interfaces between ionic/polar materials, which encompass most colloidal semiconductors. These include the use of pre-screening candidate models based on charge balance at the interface and the use of a classical potential for fast energy evaluations, with parameters automatically calculated based on the input bulk structures. These developments are validated for perovskite-based CsPbBr 3 /Pb 4 S 3 Br 2 heterostructures, where Ogre produces interface models in excellent agreement with density functional theory and experiments. Furthermore, we use Ogre to rationalize the templating effect of CsPbCl 3 on the growth of lead sulfochlorides, where perovskite seeds induce the formation of Pb 4 S 3 Cl 2 rather than Pb 3 S 2 Cl 2 due to better epitaxial compatibility. Finally, combining Ogre simulations with experimental data enables us to unravel the structure and composition of the hitherto unsolved CsPbBr 3 /Bi x Pb y S z interface, and to assign a structure to several other reported metal halide- and oxide-based interfaces. The Ogre package is available on GitHub or via the OgreInterface desktop application, available for Windows, Linux, and Mac.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗