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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Crystal Structure of an Anisotropic Pyrope Garnet That Contains Two Cubic Phases

The crystal structure of two different samples of pyrope garnet, ideally Mg 3 Al 2 Si 3 O 12 , from South Africa was refined using the Rietveld method, space group Ia3¯d, and monochromatic synchrotron high-resolution powder X-ray diffraction (HRPXRD) data. Sample 1 from Wesselton Mine is a single cubic phase and is optically isotropic. Electron-probe microanalysis (EPMA) provided an average composition {Mg 2.30 Fe 2+ 0.26 Ca 0.42 Mn 2+ 0.02 } Σ3 [Al 1.53 Fe 3+ 0.06 Cr 3+ 0.40 Ti 4+ 0.01 Fe 2+ 0.01 ] Σ2 Si 3 O 12 , which contains a significant amount of Cr cations. The unit-cell parameter (Å) and bond distances (Å) are a = 11.56197(1) Å, average = 2.2985, Al-O = 1.9101(4), and Si-O = 1.6343(3) Å. Sample 2 from De Beers Diamond Mine has an average composition {Mg 2.33 Fe 2+ 0.33 Ca 0.33 Mn 2+ 0.01 } Σ3 [Al 1.73 Fe 3+ 0.12 Cr 3+ 0.06 Ti 4+ 0.05 Fe 2+ 0.05 ] Σ2 Si 3 O 12 and is a fine-scale intergrowth of two cubic phases. The weight percentage, unit-cell parameter (Å), and bond distances (Å) for phase 2a are 62.2(1)%, a = 11.56185(1) Å, average = 2.3006, Al-O = 1.9080(4), Si-O = 1.6334(4) Å. The corresponding values for phase 2b are 37.8(1)%, a = 11.53896(1) Å, average = 2.2954, Al-O = 1.9020(6), Si-O = 1.6334(6) Å. The two cubic phases in sample 2 cause the crystal to be optically anisotropic because of strain induce birefringence. The unit-cell parameter and bond distances for sample 1 are similar to those in phase 2a.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structure of ice VII with Hirshfeld atom refinement

In the refinement of the crystal structures of ice, the best results obtained so far have been with neutron diffraction because the most troublemaking aspects are the hydrogen atoms. In nine out of twenty ice structures, the hydrogen atoms are disordered, which makes proper refinement more difficult. In our previous paper describing the structure of ice VI we proved that, using Hirshfeld atom refinement (HAR) based on synchrotron X-ray data, it is possible to obtain results comparable with those from neutron experiments. In this work, we investigate another structure of high-pressure disordered ice, cubo-ice (ice VII). Single crystals of cubo-ice were grown under pressure in diamond anvil cells. X-ray diffraction measurements were conducted at a synchrotron source facility (APS, University of Chicago, USA) as well as on our regular in-house laboratory diffractometer with Ag radiation. The data collected were further refined with HAR. Comparison of the structural parameters obtained with those derived from neutron diffraction showed very good agreement in terms of bond lengths and fairly good agreement in terms of hydrogen atom ADPs. We were also able to perform unconstrained refinements with various split-atom models.

Chemistry↗
DOE OSTI2020

On single-crystal neutron-diffraction in DACs: quantitative structure refinement of light elements on SNAP and TOPAZ

Quantitative single crystal neutron-diffraction in diamond anvil cells has so far been limited by the neutron flux available at the various neutron sources. As a result, highly precise measurements of the exact position of light elements have not been possible preventing, for example, structural studies of hydrogen and hydrogen bonds under pressure. Here we report experiments carried out on SNAP at the Spallation Neutron Source (ORNL, TN, USA) to explore the possibility and current limits of such studies. Furthermore, we benchmarked the obtained data quality with reference experiments carried out on TOPAZ, a dedicated single-crystal instrument.We show that measuring single-crystal diffraction intensities on SNAP is possible to such a precision that we are able to resolve the hydrogen bonds in potassium dideuterium phosphate (DKDP) as well as in ice VI.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Powder X-ray diffraction of fluorometholone, C 22 H 29 FO 4

Commercial fluorometholone, CAS #426-13-1, crystallizes in the monoclinic space group P 2 1 (#4) with a = 6.40648(2), b = 13.43260(5), c = 11.00060(8) Å, β = 92.8203(5)°, V = 945.517(5) Å 3 , and Z = 2. A reduced cell search in the Cambridge Structural Database yielded one previous structure determination, using single-crystal data at 292 K. In this work, the sample was ordered from the United States Pharmacopeial Convention (Lot # R032K0) and analyzed as-received. The room temperature (295 K) crystal structure was refined using synchrotron ( λ = 0.412826 Å) powder diffraction data and optimized using density functional theory (DFT) techniques. Hydrogen positions were included as a part of the structure and were re-calculated during the refinement. The diffraction data were collected on beamline 11-BM at the Advanced Photon Source, Argonne National Laboratory, and the powder X-ray diffraction pattern of the compound has been submitted to ICDD® for inclusion in the Powder Diffraction File™. The agreement of the Rietveld-refined and DFT-optimized structures is excellent; the root-mean-square Cartesian displacement is 0.060 Å. In addition to the O–H⋯O hydrogen bonds observed by Park et al. (Park, Y. J., Lee, M. Y., and Cho, S. I. ( 1992 ). “Fluorometholone,” J. Korean Chem. Soc. 36 , 812–817), C–H⋯O hydrogen bonds contribute to the crystal energy.

Gonzalez, Diana↗
DOE OSTI2020

One Structure, Two Elements—LuGe 2 Superconductor vs Ordinary Metallic Conductor LuSn 2 . A Case Study on How Site-Selective Germanium for Tin Atom Substitution Leads to Modulating of the Charge Distribution

The substitution of chemically similar elements in a given crystal structure is an effective way to enhance physical properties, but the understanding on such improvements is usually impeded because the substitutions are random, and the roles of the different atoms cannot be distinguished by crystallographic symmetry. Herein, we provide a detailed crystallographic analysis and property measurements for the continuous solid solutions LuGe x Sn 2–x (0 < x < 2). The results show that there is no apparent change of the global symmetry, with the end-members LuGe 2 and LuSn 2 , as well as the intermediate LuGe x Sn 2–x compositions adopting the ZrSi 2 type structure (space group Cmcm, Pearson index oC12). Yet, the refinements of the crystal structures from single-crystal X-ray diffraction data show that Ge–Sn atom substitutions are not random, but occur preferentially at the zig-zag chain. The patterned distribution of two group 14 elements leads to a significant variation in chemical bonding and charge ordering within the other structural fragment, the 2D square nets, thereby resulting in tuned electron transport. The enhancement is greater than the typical Bloch-Gruneisen model, and more akin to the parallel-resistor model. Magnetization measurements on single crystals show bulk superconductivity in all LuGe x Sn 2–x samples with shielding fractions as high as 90%. Specific heat data confirm the effect to originate from residual metallic tin in the material, indicating that Sn atom substitutions in the 2D square nets cause disruptions of the hypervalent bonding and local anisotropy, which ultimately leads to vanishing of the superconducting state in the end-member LuGe 2 . This work sheds light on how the complexity in chemical interactions by two different carbon congeners leads to changes in the physical properties and how they can be correlated with the induced charge distribution. Furthermore, these studies also provide a general approach to modulation of charge density, and thus, of emerging physical properties in other classes of intermetallic systems based on the main-group elements of groups 13 to 15.

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

Crystal structure of danofloxacin mesylate (C 19 H 21 FN 3 O 3 )(CH 3 O 3 S)

The crystal structure of danofloxacin mesylate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Danofloxacin mesylate crystallizes in space group P1 (#1) with a = 6.77474(8), b = 12.4973(4), c = 12.82826(28) Å, α = 84.8709(29), β = 87.7501(10), γ = 74.9916(4)°, V = 1044.723(11) Å 3 , and Z = 2. The protonation of the danofloxacin cations was established by the analysis of potential intermolecular interactions and differs from that expected from isolated-cation calculations. The crystal structure consists of alternating layers of cations and anions parallel to the ac-plane. There is parallel stacking of the oxoquinoline rings along the a-axis. The expected N–H∙∙∙O hydrogen bonds between the cations and anions are not present. Each cation makes an N–H∙∙∙O hydrogen bond with the other cation, resulting in zig-zag chains along the a-axis. Both cations have strong intramolecular O–H∙∙∙O hydrogen bonds. There are several C–H∙∙∙O hydrogen bonds between the danofloxacin cations and mesylate anions. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2023

Symmetry-mode analysis for local structure investigations using pair distribution function data

Symmetry-adapted distortion modes provide a natural way of describing distorted structures derived from higher-symmetry parent phases. Structural refinements using symmetry-mode amplitudes as fit variables have been used for at least ten years in Rietveld refinements of the average crystal structure from diffraction data; more recently, this approach has also been used for investigations of the local structure using real-space pair distribution function (PDF) data. Here, the value of performing symmetry-mode fits to PDF data is further demonstrated through the successful application of this method to two topical materials: TiSe2, where a subtle but long-range structural distortion driven by the formation of a charge-density wave is detected, and MnTe, where a large but highly localized structural distortion is characterized in terms of symmetry-lowering displacements of the Te atoms. Here, the analysis is performed using fully open-source code within the DiffPy framework via two packages developed for this work: isopydistort, which provides a scriptable interface to the ISODISTORT web application for group theoretical calculations, and isopytools, which converts the ISODISTORT output into a DiffPy-compatible format for subsequent fitting and analysis. These developments expand the potential impact of symmetry-adapted PDF analysis by enabling high-throughput analysis and removing the need for any commercial software.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Higher Dimensionality in the Mg–Co–B System: Synthesis and Structure of Incommensurate Composite Mg 1+ε Co 4 B 4

Guided by high-temperature in situ X-ray diffraction, the discovery and synthesis of Mg 1+ε Co 4 B 4 (ε ≈ 0.272) using a MgH 2 hydride precursor is reported, along with a detailed crystal structure description and measurement of magnetic properties. The mismatch in lattice periodicities between Mg and Co–B substructures places Mg 1+ε Co 4 B 4 in the family of incommensurate composite crystals and prompted structural refinement in a (3 + 1)-dimensional model. The structure of Mg 1+ε Co 4 B 4 (P4 2 /ncm(00γ)s00s, a = 6.75847(7) Å, c = 3.94007(8) Å, q = (0, 0, 1.2721(3))) was refined from neutron powder diffraction and high-resolution powder X-ray diffraction data and confirmed by scanning transmission electron microscopy and electron diffraction. Mg 1+ε Co 4 B 4 is isostructural to Nd 1+ε Fe 4 B 4 and several related ternary borides with 0.07 ≤ ε ≤ 0.17, with Mg occupying the rare-earth site. Satellite reflections in the electron diffraction patterns hinted at positional modulation of the transition metal–boron substructure by Mg atoms, but this could not be refined from the neutron or X-ray diffraction data. Low-temperature magnetic measurements show no indications of long-range magnetic ordering or superconductivity down to 5 K. DFT calculations confirmed the absence of a magnetically ordered ground state and the stability of a 5:4 supercell (ε = 0.25) relative to the fully commensurate structure. Neutron diffraction and synthesis from elemental Mg demonstrated that Mg 1+ε Co 4 B 4 is not a hydrogen-stabilized phase. Mg 1+ε Co 4 B 4 represents the second compound reported in the Mg–Co–B system and the first superspace symmetry model of a Nd 1+ε Fe 4 B 4 -type incommensurate composite compound refined from powder diffraction data.

chemical structure↗
DOE OSTI2020

Structural Assessment of Fluorine, Chlorine, Bromine, Iodine, and Hydroxide Substitutions in Lead Arsenate Apatites (Mimetites)–Pb 5 (AsO 4 ) 3 X

Five lead-arsenate apatites (mimetites)-Pb 5 (AsO 4 ) 3 X—where X denotes fluorine (F), chlorine (Cl), bromine (Br), iodine (I), and hydroxide (OH)—were synthesized via precipitation from aqueous solutions. The crystal structures were determined through Rietveld refinement of powder synchrotron X-ray data. All the compounds crystallized in the hexagonal class symmetry (space group P6 3 /m). The Rietveld refinement indicated that mimetite-Cl, -Br, -I, and -OH had an anion deficiency at position X. Substitution of halogens in a mimetite structure brought about systematic changes in unit-cell parameters, interatomic distances, and metaprism twist angles φ, proportional to the substituted halogen’s ionic radius. Mimetite-OH did not follow the linear correlations determined within the series. Twist angle φ, a useful device for monitoring changes in apatite topology, ranged from 20.34° for mimetite-F to 11.42° for mimetite-I. The geometric method has been proposed for determining the diameter of hexagonal channels hosting halogens in apatites. A comparison of the results with halogenated pyromorphites showed similar systematic trends: the substitutions in mimetites have comparable effect on the interatomic distances as in their phosphorous analogues.

58 GEOSCIENCES↗
DOE OSTI2025

Machine learning of 27Al NMR electric field gradient tensors for crystalline structures from DFT

NMR crystallography has emerged as a promising technique for the determination and refinement of atomic coordinates in crystal structures. The crystal structure of compounds containing quadrupolar nuclei, such as 27Al, can be improved by directly comparing solid-state NMR measurements to DFT computations of the electric field gradient (EFG) tensor. The non-negligible computational cost of these first-principles calculations limits the applicability of this method to all but the most well-defined structures. We developed a fast, low-cost machine learning model to predict EFG parameters based on local structural motifs and elemental parameters. We computed 8081 EFG tensors from 1681 27Al crystalline solids using DFT and benchmarked them against 105 experimentally measured 27Al sites. Surprisingly, simple local geometric features dominate the predictive performance of the resulting random-forest model, yielding an R2 value of 0.98 and an RMSE of 0.61 MHz for CQ, the quadrupolar coupling constant. This model accuracy should enable pre-refining future structural assignments before finally validating with first-principles calculations. Such a catalogue of 27Al NMR tensors can serve as a tool for researchers assigning complex NMR spectra influenced by the nuclear electric quadrupole interaction.

Sun, He↗
DOE OSTI2024

Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment

Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid–base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.

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

Evaluating the pressure dependence of PZT structures using a virtual reality environment

Pb–Zr–Ti–O (PZT) perovskites span a large solid-solution range and have found widespread use due to their piezoelectric and ferroelectric properties that also span a large range. Crystal structure analysis via Rietveld refinement facilitates materials analysis via the extraction of the structural parameters. These parameters, often obtained as a function of an additional dimension (e.g., pressure), can help to diagnose materials response within a use environment. Often referred to as “ in-situ ” studies, these experiments provide an abundance of data. Viewing structural changes due to applied pressure conditions can give much-needed insight into materials performance. However, challenges exist for viewing/presenting results when the details are inherently three-dimensional (3D) in nature. For PZT perovskites, the use of polyhedra (e.g., Zr/Ti–O 6 octahedra) to view bonding/connectivity is beneficial; however, the visualization of the octahedra behavior with pressure dependence is less easily demonstrated due to the complexity of the added pressure dimension. We present a more intuitive visualization by projecting structural data into virtual reality (VR). We employ previously published structural data for Pb 0.99 (Zr 0.95 Ti 0.05 ) 0.98 Nb 0.02 O 3 as an exemplar for VR visualization of the PZT R3c crystal structure between ambient and 0.62 GPa pressure. This is accomplished via our in-house CAD2VR™ software platform and the new CrystalVR plugin. The use of the VR environment enables a more intuitive viewing experience, while enabling on-the-fly evaluation of crystal data, to form a detailed and comprehensive understanding of in-situ datasets. Discussion of methodology and tools for viewing are given, along with how recording results in video form can enable the viewing experience.

Rodriguez, Mark A. (ORCID:0000000269405044)↗
DOE OSTI2025

Bridging Experiment and Theory to Reveal Compounds in K–Zn(Cd)–Bi Systems

This study investigates the facile hydride synthesis method guided by theoretical predictions to explore the K–T–Bi (T = Zn, Cd) phase spaces. Using an adaptive genetic algorithm (AGA) and density functional theory (DFT), candidate compositions are identified for experimental validation via a facile hydrides route, permitting experimental screening of K–Zn–Bi and “empty” K–Cd–Bi systems. The previously reported KZnBi and KZn 2 Bi 2 are synthesized alongside newly discovered KCdBi and KCd 2 Bi 2 . While the AGA and DFT predict the stability of these compounds, structural predictions align with the experiment only for KZnBi and KZn 2 Bi 2 . Single-crystal X-ray structure refinements confirm that KZnBi and KZn 2 Bi 2 adopt the hexagonal ZrBeSi- and tetragonal ThCr 2 Si 2 -structure types, respectively. KCdBi has tetragonal PbClF-structure type and KCd 2 Bi 2 belongs to the ThCr 2 Si 2 -structure type. A trend based on the ratio of the metal ionic radii allows to rationalize variation in the structure types within the ATBi family (A = Li–Cs), correctly identifying KCdBi as isostructural to NaZnBi. Thermal stability studied by high-temperature powder X-ray diffraction reveals that Zn-containing compounds melt at higher temperatures (821 K for KZn 2 Bi 2 ) than Cd-containing KCd 2 Bi 2 (635 K). This study highlights the efficacy of combining rapid synthesis techniques with predictive modeling, though structural predictions show some limitations in accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Li2[SeC2Se] · 2 NH3: A Crystalline Ammoniate with a-Se-C=C-Se- Dianion

Reaction of Li2C2 with elemental selenium in a molar ratio of 1:2 in liquid ammonia led to the formation of the ammoniate Li2[SeC2Se] ? 2 NH3. Its crystal structure was solved and refined from high-resolution synchrotron powder diffraction data (P21/c, Z = 4). It contains the ?Se-C?C-Se? anion, unprecedented in a crystalline material, whose existence was corroborated by IR/Raman spectra and electronic-structure theory, showing an almost perfect agreement with calculated spectra. Elaborated magnetic-bottle and velocity-map imaging photoelectron spectroscopic investigations show that the ?Se-C?C-Se? radical anion can be transferred to the gas phase, where it was analyzed by NIPE (Negative Ion Photoelectron) and VMI (Velocity-Map Imaging) spectra, which correlate nicely with simulated spectra based on 2?u ? 3Sg – and 2?u ?1Sg + transitions including spin-orbit couplings

Hetzert, Marc↗
DOE OSTI2026

NeuDiff Agent: a governed AI workflow for single-crystal neutron crystallography

Large-scale facilities increasingly face analysis and reporting latency as a limiting step in scientific throughput, particularly for structural studies that require iterative reduction, integration, refinement and validation. To improve the time to result and analysis efficiency, NeuDiff Agent is introduced as a governed, tool-using AI workflow for TOPAZ at the Spallation Neutron Source. NeuDiff Agent takes instrument data through reduction, integration, refinement and validation to a validated crystal structure and a publication-ready CIF. NeuDiff Agent coordinates established crystallographic tools under explicit governance by restricting actions to allowlisted tools, enforcing fail-closed verification gates at key workflow boundaries, and capturing complete provenance for inspection, auditing and controlled replay. The present benchmark is limited to structural crystallography for periodic structures; magnetic structure analysis and incommensurate or superspace refinement are outside the scope of the current workflow. Performance is assessed using a fixed prompt protocol and repeated end-to-end runs with two large language model backends, with user and machine time partitioned and intervention burden and recovery behaviors quantified under gating. In a reference-case benchmark, NeuDiff Agent reduces wall time from 435 min (manual) to 86.5 ± 4.7 to 94.4 ± 3.5 min (4.6–5.0× faster) while producing a validated CIF with no checkCIF level A or B alerts. These results establish a practical route to deploy agentic AI in facility crystallography while preserving traceability and publication-facing validation requirements.

Xiao, Zhongcan [ORNL] (ORCID:0000000220761961)↗
DOE OSTI2022

Ferromagnetic MnBi 4 Te 7 obtained with low-concentration Sb doping: A promising platform for exploring topological quantum states

The tuning of the magnetic phase, chemical potential, and structure is crucial to observe diverse exotic topological quantum states in Mn Bi 2 Te 4 (Bi 2 Te 3 ) m (m = 0–3). Here we show a ferromagnetic (FM) phase with a chiral crystal structure in Mn (Bi 1–x Sb x ) 4 Te 7 , obtained via tuning the growth conditions and Sb concentration. Unlike previously reported Mn (Bi 1–x Sb x ) 4 Te 7 , which exhibits FM transitions only at high Sb doping levels, our samples show FM transitions (T C = 13.5 K) at 15%–27% doping levels. Furthermore, our single-crystal x-ray-diffraction structure refinements find Sb doping leads to a chiral structure with the space group of P3, contrasted with the centrosymmetric $P\bar{3}m1$ crystal structure of the parent compound MnBi 4 Te 7 . Through angle-resolved photoemission spectroscopy measurements, we also demonstrated that the nontrivial band topology is preserved in the Sb-doped FM samples. Given that the nontrivial band topology of this system remains robust for low Sb doping levels, our success in making FM Mn(Bi 1–x Sb x ) 4 Te 7 with x = 0.15, 0.175, 0.2, and 0.27 paves the way for realizing the predicted topological quantum states, such as the axion insulator and Weyl semimetals. Additionally, we also observed magnetic glassy behavior in both antiferromagnetic MnBi 4 Te 7 and FM Mn (Bi 1–x Sb x )4 Te 7 samples, which we believe originates from cluster spin-glass phases coexisting with long-range antiferromagnetic/FM orders. Further, we have also discussed how the antisite Mn ions impact the interlayer magnetic coupling and how FM interlayer coupling is stabilized in this system.

36 MATERIALS SCIENCE↗
DOE OSTI2021

The crystal structure of a new calcium aluminate phase containing formate

A new calcium aluminate phase containing formate ions was synthesized and its crystal structure determined. This new phase is indicated as M-phase and was firstly observed in Portland cement pastes hydrated in presence of Ca-formate and in excess of water. The crystal structure of the M-phase was successfully solved in the R-3 space group of the trigonal system on the basis of synchrotron X-ray single crystal diffraction data. The structural model was confirmed by Rietveld refinement of the powder diffraction data acquired on the synthesized pure sample. The crystal structure of the M-phase is similar to that of ettringite, being characterized by columns of AlO{sub 6} octahedra alternating with groups of three edge-sharing CaO{sub 7} polyhedra. The formate ions (HCOO){sup −} share two oxygens with Ca polyhedra and are located in the interspace between the columns. The crystal structure of the M-phase testifies the strong interaction occurring between small organic molecules as formate and the calcium aluminate components of Portland cement.

36 MATERIALS SCIENCE↗