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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

First-Principles Evaluation of Proton Hopping in Tetrahedral Oxide Motifs

Proton-conducting oxides (PCOs) are important materials used as ionic conductors for energy conversion technologies. Existing research efforts on PCO optimization and discovery generally focus on complex perovskite-based oxides that require doping and alloying to engineer oxygen deficiency and high proton conductivity. However, the variety of chemical compositions and coordination environments in oxides poses challenges for efficient materials design. In this computational study, we construct a database of simplified motifs to elucidate the relationship between fundamental materials chemistry and proton kinetics. Specifically, we focus on the zincblende crystal structure as a proxy for tetrahedral metal–oxide (M–O) coordination environments. We systematically quantified the effects of cation type, oxidation states, and M–O bond lengths on the proton hopping barrier, and found that strong M–O bonds and metal cations with large and variable oxidation states (e.g., Mo 6+ , V 5+ ) lead to smaller proton hopping barriers. By mapping the candidate cations and their preferred bond geometries onto materials databases such as the Inorganic Crystal Structure Database (ICSD) and Materials Project, we identified real materials containing the corresponding metal–oxide units. In general, we observed good agreement between the calculated proton hopping barriers obtained in real crystal structures and those predicted by our motif database. We also discuss the limitations of our model and possible future extensions to improve its predictive capabilities. Overall, our model provides a first step for the rational design and quick screening of energy-efficient PCOs.

organic↗
DOE OSTI2022

Scalable Synthesis and Characterization of Multilayer γ-Graphyne, New Carbon Crystals with a Small Direct Band Gap

γ-Graphyne is the most symmetric sp 2 /sp 1 allotrope of carbon, which can be viewed as graphene uniformly expanded through the insertion of two-carbon acetylenic units between all the aromatic rings. To date, synthesis of bulk γ-graphyne has remained a challenge. In this work, we report the synthesis of multilayer γ-graphyne through crystallization-assisted irreversible cross-coupling polymerization. A comprehensive characterization of this new carbon phase is described, including synchrotron powder X-ray diffraction, electron diffraction, lateral force microscopy, Raman spectroscopy, infrared spectroscopy, and cyclic voltammetry. Experiments indicate that γ-graphyne is a 0.48 eV band gap semiconductor, with a hexagonal a-axis spacing of 6.88 Å and an interlayer spacing of 3.48 Å, which is consistent with theoretical predictions. The observed crystal structure has an aperiodic sheet stacking. The material is thermally stable up to 240 °C but undergoes transformation at higher temperatures. While conventional 2D polymerization and reticular chemistry rely on error correction through reversibility, we demonstrate that a periodic covalent lattice can be synthesized under purely kinetic control. The reported methodology is scalable and inspires extension to other allotropes of the graphyne family.

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

Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase

Designing realistic quantum mechanical (QM) models of enzymes is dependent on reliably discerning and modeling residues, solvents, and cofactors important in crafting the active site microenvironment. Interatomic van der Waals contacts have previously demonstrated usefulness toward designing QM-models, but their measured values (and subsequent residue importance rankings) are expected to be influenceable by subtle changes in protein structure. Using chorismate mutase as a case study, this work examines the differences in ligand-residue interatomic contacts between an x-ray crystal structure and structures from a molecular dynamics simulation. Select structures are further analyzed using symmetry adapted perturbation theory to compute ab initio ligand-residue interaction energies. The findings of this study show that ligand-residue interatomic contacts measured for an x-ray crystal structure are not predictive of active site contacts from a sampling of molecular dynamics frames. In addition, the variability in interatomic contacts among structures is not correlated with variability in interaction energies. However, the results spotlight using interaction energies to characterize and rank residue importance in future computational enzymology workflows.

Chemistry↗
DOE OSTI2022

Reflections on one million compounds in the open quantum materials database (OQMD)

Abstract Density functional theory (DFT) has been widely applied in modern materials discovery and many materials databases, including the open quantum materials database (OQMD), contain large collections of calculated DFT properties of experimentally known crystal structures and hypothetical predicted compounds. Since the beginning of the OQMD in late 2010, over one million compounds have now been calculated and stored in the database, which is constantly used by worldwide researchers in advancing materials studies. The growth of the OQMD depends on project-based high-throughput DFT calculations, including structure-based projects, property-based projects, and most recently, machine-learning-based projects. Another major goal of the OQMD is to ensure the openness of its materials data to the public and the OQMD developers are constantly working with other materials databases to reach a universal querying protocol in support of the FAIR data principles.

08 HYDROGEN↗
NASA NTRS1995

Effect of Stacking Faults on the X-Ray Diffraction Profiles of Beta-SiC Powders

X-ray diffraction patterns or beta-SiC (3C or the cubic polytype or sic) powders often exhibit an additional peak at d = 0.266 nm, high background intensity around the (111) peak, and relative intensities for peaks which differ from those predicted from the crystal structure. Computer simulations were used to show that all these features are due to stacking faults in the powders and not due to the presence of other polytypes in the powders. Such simulations allow diffraction patterns to be generated for different types, frequencies, and spatial distribution or faults. Comparison of the simulation results to the XRD data indicates that the B-SiC particles consist either of heavily faulted clusters distributed irregularly between regions that have only occasional faults or twins, or the powders consist of two types of particles with different populations of faults: those with a high density of faults and those with only twins or occasional faults. Additional information is necessary to determine which description is correct. However, the simulation results can be used to rule out certain fault configurations.

Pujar, Vijay V.↗
DOE OSTI2025

Dimensional Reduction Guides Electronic Structure Evolution in the A n Cu 4–n SnS 4 Semiconductor Series

The search for new functional materials with tunable properties remains a central challenge in chemistry, particularly for applications in energy and electronics. In this work, we present a framework for predictive crystal design in alkali metal chalcogenides that enables controlled dimensional reduction of a parent covalent motif, yielding a broad range of electronic structures, which systematically evolve from one parent to the other. We present 11 new members of the A n Cu 4–n SnS 4 family (A = alkali metal; n = 0–4), which reduce the three-dimensional (3D) covalent network of Cu 4 SnS 4 into various 3D, 2D, 1D, and 0D [Cu 4–n SnS 4 ] n− motifs through the substitution of Cu with alkali metals of various radii. The end members of the family set the range in achievable band gaps at 0.99 eV for fully covalent Cu 4 SnS 4 (n = 0) and 3.38 eV for K 4 SnS 4 (n = 4) with 0D [SnS 4 ] n− tetrahedra. As the dimensionality of [Cu 4–n SnS 4 ] n− systematically reduces within A n Cu 4–n SnS 4 (n = 1–3), a stepwise increase in band gap energy occurs through a gradual decrease in the energy of the valence band maximum and an increase in the conduction band minimum, with an increase in the effective masses of charge carriers. Furthermore, irrespective of the alkali metal, the thermal stability decreases with decreasing [Cu 4–n SnS 4 ] n− dimensionality within the quaternary members. Most importantly, we demonstrate that predictable crystal structure and property evolution for a given composition space is possible by deriving a general formula based on substituting the covalent metals of a parent structure with alkali metals.

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

Protein-ligand binding affinity prediction using multi-instance learning with docking structures

Recent advances in 3D structure-based deep learning approaches demonstrate improved accuracy in predicting protein-ligand binding affinity in drug discovery. These methods complement physics-based computational modeling such as molecular docking for virtual high-throughput screening. Despite recent advances and improved predictive performance, most methods in this category primarily rely on utilizing co-crystal complex structures and experimentally measured binding affinities as both input and output data for model training. Nevertheless, co-crystal complex structures are not readily available and the inaccurate predicted structures from molecular docking can degrade the accuracy of the machine learning methods. We introduce a novel structure-based inference method utilizing multiple molecular docking poses for each complex entity. Our proposed method employs multi-instance learning with an attention network to predict binding affinity from a collection of docking poses. We validate our method using multiple datasets, including PDBbind and compounds targeting the main protease of SARS-CoV-2. The results demonstrate that our method leveraging docking poses is competitive with other state-of-the-art inference models that depend on co-crystal structures. This method offers binding affinity prediction without requiring co-crystal structures, thereby increasing its applicability to protein targets lacking such data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Symmetry in Seeded Metal Nanocrystal Growth

Symmetry underpins the structure and function of the world around us and is also captured in modern nanomaterials, where changing the symmetry of a nanocrystal or the interparticle spacing and orientation of nanocrystal building blocks in a superlattice can give new function. However, the synthesis and assembly of nanocrystals have been limited largely to simple compositions and structures. It remains a grand challenge to achieve nanocrystals with compositional and structural complexity while maintaining the monodispersity required for their use. This Account will illustrate through recent examples that seeded methods enable the synthesis of compositionally and structurally complex multimetallic crystals with defined and predictable symmetries for applications in plasmonics and catalysis. This outcome arises because the barrier for heterogeneous nucleation (i.e., seeded) is lower than that of homogeneous nucleation, where seeds can serve as preferential sites for the growth of complex structures and crystal phases. Our analysis begins by considering metal overgrowth from single-crystalline seeds of different shapes and symmetries, where the kinetics of adatom addition to seeds relative to their diffusion across seeds accounts for the expressed nanocrystal shapes. These results are then compared to overgrowth from seeds with different internal structures (i.e., planar defects), where the relationships between nanocrystal size and volumetric strain energy and surface energy are discussed. A major finding from this analysis is that often the underlying symmetry of seeds can be predictably transferred to the final crystals during overgrowth processes. Consequences of this finding are the predictable syntheses of crystals with different hierarchies akin to snowcrystals as well as nanocrystals with complex compositions (e.g., quaternary nanoparticles). Yet, there are subtle aspects to seeded growth that pave a path toward examples where nanocrystal symmetry has been reduced compared to the original seeds in a controlled manner. As we found, both the concentrations of metal precursors and capping agents can impact whether symmetry is transferred or reduced during overgrowth. Examples from our laboratory will be placed in context to other reported strategies for symmetry breaking. As will be argued, understanding what conditions favor symmetry preservation versus symmetry reduction during seeded crystal growth is central to accessing next-generation crystal forms. The Account concludes by outlining synthetic challenges associated with forming nanoscale heterostructures with precise 3-D placement of different materials within a given nanocrystal as well as facet control within different material domain and interface engineering. Furthermore, we envision meeting these challenges through regioselective and chemoselective seeded syntheses for which a foundation is outlined herein.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture

Beetroot is a homodimeric in vitro selected RNA that binds and activates DFAME, a conditional fluorophore derived from GFP. It is 70% sequence-identical to the previously characterized homodimeric aptamer Corn, which binds one molecule of its cognate fluorophore DFHO at its interprotomer interface. We have now determined the Beetroot-DFAME co-crystal structure at 1.95 Å resolution, discovering that this RNA homodimer binds two molecules of the fluorophore, at sites separated by ~30 Å. In addition to this overall architectural difference, the local structures of the non-canonical, complex quadruplex cores of Beetroot and Corn are distinctly different, underscoring how subtle RNA sequence differences can give rise to unexpected structural divergence. Through structure-guided engineering, we generated a variant that has a 12-fold fluorescence activation selectivity switch toward DFHO. Beetroot and this variant form heterodimers and constitute the starting point for engineered tags whose through-space inter-fluorophore interaction could be used to monitor RNA dimerization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

MarK, a Novosphingobium aromaticivorans kinase required for catabolism of multiple aromatic monomers

The aromatic compounds used in a variety of industrial products are currently obtained from nonrenewable petroleum sources. Alternatively, the plant polymer lignin is an abundant renewable source of aromatics, and its depolymerization generates a variety of products that can include acetovanillone, a vanillin derivative containing an acetyl side chain. The Alphaproteobacterium Novosphingobium aromaticivorans DSM12444 can metabolize several chemically modified aromatics in deconstructed lignin, but not acetovanillone. In this work, adaptive laboratory evolution identified a single amino acid change in the previously uncharacterized gene product Saro_1862 that is necessary and sufficient for N. aromaticivorans growth with acetovanillone as a sole growth substrate, as well as other aromatic monomers not metabolized by wild-type cells. We show that a glutamate (E) to lysine (K) substitution at amino acid residue 16 of Saro_1862 results in a ~1600-fold increase in the rate of ATP-dependent acetovanillone phosphorylation. We also find that recombinant Saro_1862 E16K phosphorylates several other aromatic compounds in vitro , defining the first reported catalytic activity for the widespread UPF0261 protein domain contained in Saro_1862. Thus, we propose naming Saro_1862 MarK, for multiple aromatic kinase. A 1.57 Å crystal structure of MarK E16K predicts that the E16K substitution lies in a potential ATP binding site, suggesting how this amino acid change increased catalytic activity. A search for homologs of MarK and other proteins required for acetovanillone degradation predicts that this pathway for aromatic metabolism exists throughout the bacterial phylogeny.

Novosphingobium↗
DOE OSTI2022

Novel fold of rotavirus glycan-binding domain predicted by AlphaFold2 and determined by X-ray crystallography

The VP8* domain of spike protein VP4 in group A and C rotaviruses, which cause epidemic gastroenteritis in children, exhibits a conserved galectin-like fold for recognizing glycans during cell entry. In group B rotavirus, which causes significant diarrheal outbreaks in adults, the VP8* domain (VP8*B) surprisingly lacks sequence similarity with VP8* of group A or group C rotavirus. Here, by using the recently developed AlphaFold2 for ab initio structure prediction and validating the predicted model by determining a 1.3-Å crystal structure, we show that VP8*B exhibits a novel fold distinct from the galectin fold. This fold with a β-sheet clasping an α-helix represents a new fold for glycan recognition based on glycan array screening, which shows that VP8*B recognizes glycans containing N-acetyllactosamine moiety. Although uncommon, our study illustrates how evolution can incorporate structurally distinct folds with similar functionality in a homologous protein within the same virus genus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Graph neural networks predict energetic and mechanical properties for models of solid solution metal alloy phases

Here, we developed a PyTorch-based architecture called HydraGNN that implements graph convolutional neural networks (GCNNs) to predict the formation energy and the bulk modulus for models of solid solution alloys for various atomic crystal structures and relaxed volumes. We trained the GCNN surrogate model on a dataset for nickel–niobium (NiNb) generated by the embedded atom model (EAM) empirical interatomic potential for demonstration purposes. The dataset was generated by calculating the formation energy and the bulk modulus as a prototypical elastic property for optimized geometries starting from initial body-centered cubic (BCC), face-centered cubic (FCC), and hexagonal compact packed (HCP) crystal structures, with configurations spanning the possible compositional range for each of the three types of initial crystal structures. Numerical results show that the GCNN model effectively predicts both the formation energy and the bulk modulus as function of the optimized crystal structure, relaxed volume, and configurational entropy of the model structures for solid solution alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Influence of shape on crystal structure and optical properties of heterocyclic conjugated molecules

Organic optoelectronics are increasingly important due to their tunablilty, flexibility, and solution processability. Tuning optical properties of these materials as solids relies on the balance of weak non-covalent interactions that dictate crystal structure, but are difficult to predict. Our research aims to improve our understanding of how electrostatic interactions can direct and facilitate intramolecular interactions that dictate emergent properties of crystalline materials. This paper focuses on exploring how multi-fused thiophene ring systems that are popular in modern organic optoelectronic materials impact intramolecular interactions, while also investigating the role of molecular shape. In these examples, the shape of heterocyclic systems correlate with the crystal structures: while the bent heterocyclics show no discrete and discernable intramolecular interactions, those with bent shapes interact cofacially with one of the electron poor ArF pendants by twisting the arylene ethynylene backbone. Two of the control molecules, which bear non-fluorinated benzyl ester substituents, show intramolecular edge-face interactions, and several of these molecules show clear polymorphic behavior. Furthermore, these findings further our understanding of how discrete interactions can be altered not only by electrostatics, but also by shape, allowing for increasingly nuanced control over the crystal structures and optical properties of optoelectronic materials.

Guzmán, Elisa↗
DOE OSTI2022

Structural and electronic properties of rare-earth chromites: A computational and experimental study

Here, in this work, the structural, optical, and electronic properties of rare-earth perovskites of the general formula R⁢ CrO 3 , where R⁢ represents the rare-earth Gd, Tb, Dy, Ho, Er, and Tm, have been studied in detail. These compounds were synthesized through a facile citrate route. X-ray diffraction, Raman spectroscopy, and UV-Visible spectroscopy were utilized to reveal the structural evolutions in R⁢ ⁢CrO 3 . The lattice parameters, Cr 3+ –O 2 –Cr 3+ bond angle, and CrO 6 octahedral distortions were found to strongly depend on the ionic radii of R⁢ . First-principles calculations based on density-functional theory within the generalized gradient approximation (GGA) of Perdew-Burke-Ernzerhof (PBE) and strongly constrained and appropriately normed (SCAN) meta-GGA were also employed to calculate the structural and electronic properties of R⁢ ⁢CrO 3 . The ground-state energy, lattice constants, electronic structures, and density of states of R⁢ ⁢CrO 3 were calculated. These provide some insights into the electronic characteristics of the R⁢ ⁢CrO 3 compounds. The calculated values of lattice parameters and band gaps with Hubbard U correction (SCAN+ U ) agree well with values measured experimentally and show more accuracy in predicting the ground-state crystal structure and band structure compared to PBE+ U approximation. The band gap of R⁢ ⁢CrO 3 is found to be independent of the ionic radii of R⁢ from both experiments and calculations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Glass formation during combinatorial sputtering in binary alloys

Glass formation is a complex phenomenon influenced by thermodynamic and kinetic aspects, which are often controlled by extrinsic contributions. While bulk metallic glasses are typically multicomponent alloys, binary alloys offer a simplified approach to studying glass formation. In this study, we fabricated 57 binary alloy systems through combinatorial sputtering, where each alloy system is represented in 66 different alloys. We developed an automated analysis to determine structure and composition using X-ray diffraction and energy-dispersive X-ray spectroscopy for over 3700 alloys. We found that ∼17 % of the alloys form glasses under the estimated cooling rate during sputtering of ∼10 8 K/s. Data analysis revealed that commonly used factors like atomic size ratio and heat of mixing are ineffective in predicting glass formation. However, the crystal structure mismatch of the alloys’ elements emerged as the strongest indicator of glass formation under sputtering conditions of binary alloys. Here, the differences in glass formation under slow cooling rates used for bulk glass formation and the here observed glass formation under rapid cooling rates are discussed.

Binary alloys↗
DOE OSTI2025

Nonexcitonic mechanism for electronic and structural phase transitions in Ta 2 ⁢Ni⁢(Se,S) 5

Here, we present a first-principles study based on density functional theory (DFT) on the electronic and structural properties of Ta 2 NiSe 5 , a layered transition metal chalcogenide that has been considered as a possible candidate for an excitonic insulator. Our systematic DFT results however provide a nonexcitonic mechanism for the experimentally observed electronic and structural phase transitions in Ta 2 NiSe 5 , in particular explaining why sulfur substitution of selenium reduces the distortion angle in the low-temperature phase and potassium dosing closes the gap in the electronic structure. Moreover, the calculations show that these two effects couple to each other. Further, our first-principles calculations predict several changes in both the crystal structure and electronic structure under the effects of uniform charge dosing and uniaxial strain, which could be tested experimentally.

Tang, Weichen [University of California, Berkeley,↗
DOE OSTI2026

A chemical bonding based descriptor for predicting the role of anharmonicity induced by quantum nuclear effects in hydride superconductors

Quantum nuclear effects (QNEs) can significantly alter a material’s crystal structure and phonon spectra, impacting properties such as thermal conductivity and superconductivity. However, predicting a priori whether these effects will enhance or suppress superconductivity, or destabilize a structure, remains a grand challenge. Herein, we address this unresolved problem by introducing two possible descriptors, based upon the integrated crystal orbital bonding index (iCOBI) or the bond valence function, to predict the influence of QNEs on a crystal lattice’s dynamic stability, phonon spectra and superconducting properties. We find that structures with atoms in symmetric chemical bonding environments exhibit greater resilience to structural perturbations induced by QNEs, while those with atoms in asymmetric bonding environments are more susceptible to structural alterations, resulting in enhanced superconducting critical temperatures.

Physical chemistry↗
DOE OSTI2024

Angle-Resolved Polarized Raman Study of Layered Cr 2 Se 3

The polarization-resolved Raman spectra of two-dimensional Cr 2 Se 3 synthesized via chemical vapor deposition (CVD) and chemical vapor transport (CVT) techniques were investigated in detail. The samples were characterized using X-ray diffraction (XRD), transmission electron microscopy (TEM), and energy-dispersive X-ray spectroscopy (EDS). A distinct polarization dependence was observed in the Raman intensity of all the Cr-Cr, Cr-Se, and Se-Se modes in both samples. The observed angle-dependent Raman intensities of each peak could be related to the crystal structure-specific Raman tensor. XRD results of the bulk Cr 2 Se 3 sample synthesized via CVT confirm its trigonal crystal structure, and the Raman peaks can be fitted using the Raman tensors for the A g and E g modes for both the parallel and crossed polarizations. However, for the Cr 2 Se 3 samples directly grown on Si/SiO 2 substrates by CVD, it was necessary to assume the triclinic crystal structure in order to explain the polarized Raman dependence of all the peaks in both parallel and crossed polarization directions. Furthermore, this is the first experimental result suggesting the existence of triclinic Cr 2 Se 3 crystal structure, which has been theoretically predicted in the Materials Project database.

36 MATERIALS SCIENCE↗