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DOE OSTI2021

Cluster Variation Method Analysis of Correlations and Entropy in BCC Solid Solutions

Solid solutions occur when multiple chemical species share sites of a common crystal lattice. Although the single site occupation is random, chemical interaction preferences bias the occupation probabilities of neighboring sites, and this bias reduced the entropy of mixing below its ideal value. Sufficiently strong bias leads to symmetry-breaking phase transitions. Here, we apply the cluster variation method to explore solid solutions on body centered cubic lattices in the context of two specific compounds that exhibit opposite ordering trends. Employing density functional theory to model the energetics, we show that CuZn exhibits an order-disorder transition to the CsCl prototype structure, while AlLi instead takes the NaTl prototype structure, and we evaluate their temperature-dependent order parameters, correlations and entropies.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Spectroscopic Signatures of Phonon Character in Molecular Electron Spin Relaxation

Spin–lattice relaxation constitutes a key challenge for the development of quantum technologies, as it destroys superpositions in molecular quantum bits (qubits) and magnetic memory in single molecule magnets (SMMs). Gaining mechanistic insight into the spin relaxation process has proven challenging owing to a lack of spectroscopic observables and contradictions among theoretical models. Here, we use pulse electron paramagnetic resonance (EPR) to profile changes in spin relaxation rates (T 1 ) as a function of both temperature and magnetic field orientation, forming a two-dimensional data matrix. For randomly oriented powder samples, spin relaxation anisotropy changes dramatically with temperature, delineating multiple regimes of relaxation processes for each Cu(II) molecule studied. We show that traditional T 1 fitting approaches cannot reliably extract this information. Single-crystal T 1 anisotropy experiments reveal a surprising change in spin relaxation symmetry between these two regimes. We interpret this switch through the concept of a spin relaxation tensor, enabling discrimination between delocalized lattice phonons and localized molecular vibrations in the two relaxation regimes. Variable-temperature T 1 anisotropy thus provides a unique spectroscopic method to interrogate the character of nuclear motions causing spin relaxation and the loss of quantum information.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Structural and functional insights into the interaction between the bacteriophage T4 DNA processing proteins gp32 and Dda

Abstract Bacteriophage T4 is a classic model system for studying the mechanisms of DNA processing. A key protein in T4 DNA processing is the gp32 single-stranded DNA-binding protein. gp32 has two key functions: it binds cooperatively to single-stranded DNA (ssDNA) to protect it from nucleases and remove regions of secondary structure, and it recruits proteins to initiate DNA processes including replication and repair. Dda is a T4 helicase recruited by gp32, and we purified and crystallized a gp32–Dda–ssDNA complex. The low-resolution structure revealed how the C-terminus of gp32 engages Dda. Analytical ultracentrifugation analyses were consistent with the crystal structure. An optimal Dda binding peptide from the gp32 C-terminus was identified using surface plasmon resonance. The crystal structure of the Dda–peptide complex was consistent with the corresponding interaction in the gp32–Dda–ssDNA structure. A Dda-dependent DNA unwinding assay supported the structural conclusions and confirmed that the bound gp32 sequesters the ssDNA generated by Dda. The structure of the gp32–Dda–ssDNA complex, together with the known structure of the gp32 body, reveals the entire ssDNA binding surface of gp32. gp32–Dda–ssDNA complexes in the crystal are connected by the N-terminal region of one gp32 binding to an adjacent gp32, and this provides key insights into this interaction.

Biochemistry & Molecular Biology↗

DOE OSTI2025

XY-like incommensurate magnetic order in Ce 2 ⁢SnS 5

We report the synthesis of single crystals of Ce 2 ⁢SnS 5 through a two-stage chemical vapor transport method. The Ce 2 ⁢SnS 5 system is a member of the orthorhombic Pbam (No. 55) space group and realizes a distorted trigonal tricapped prism (TTP) crystal field around each cerium site. We characterized the sample through orientation-dependent magnetization and heat capacity measurements to probe the magnetic anisotropy in the system characteristic of XY-like anisotropic Heisenberg model behavior. Ce 2 ⁢SnS 5 furthermore enters a zero-field ordered phase under 𝑇 𝑁 =2.4 K; powder neutron diffraction measurements reveal incommensurate magnetic order near 𝑇 𝑁 . Furthermore, the system then locks into a commensurate, two-𝑞 magnetic structure below approximately 1.2 K. This commensurate structure belongs to the Shubnikov group 𝑃⁢𝑏′⁢𝑎′⁢𝑚′ ⁡(MSG 55.359) and realizes the propagation vectors $\overrightarrow{𝑞}$ = (1/3, 0, 0) and $\overrightarrow{𝑞}$ = (0, 0, 0).

Antiferromagnetism↗

DOE OSTI2021

Carbon dioxide capture with aqueous amino acids: Mechanistic study of amino acid regeneration by guanidine crystallization and process intensification

CO 2 capture from powerplant-generated flue gas via a phase-changing process involving absorption with aqueous amino acids (e.g., glycine or sarcosine) and bicarbonate crystallization with bis-iminoguanidines (e.g., glyoxal-bis-iminoguanidine or GBIG) is investigated in this paper. This process is of high interest due to its potential to decrease the energy penalty for CO 2 capture by significantly reducing the solvent regeneration energy typically associated with aqueous amine solvents. A critical step in the proposed CO 2 capture mechanism is the regeneration of the amino acid by removal of protons and bicarbonate ions from solution through crystallization of GBIGH 2 2+ bicarbonate salt. Here, we investigated the thermodynamics and kinetics of glycine regeneration by crystallization of GBIGH 2 2+ (HCO 3 – ) 2 (H 2 O) 2 . A theoretical model was developed and compared to experimental data to simulate and predict the glycine regeneration and determine its reaction mechanism. This combined experimental and theoretical study led to the conclusion that, while the GBIGH 2 2+ bicarbonate crystallization step provides most of the thermodynamic driving force for the glycine regeneration, the rate-limiting step is the protonation of GBIG prior to crystallization. The CO 2 loading and amino acid regeneration steps were combined into a single, intensified process using a bubble column reactor. The CO 2 loading capacity of GBIG was experimentally determined to be roughly 1.36 mol CO 2 per mol GBIG. These results provide the fundamental basis for developing an effective carbon capture technology with phase-changing amino acid/guanidine absorbents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Measurement of the angular dependence of the spontaneous Raman scattering in anisotropic crystalline materials using spherical samples: Potassium dihydrogen phosphate as a case example

A specialized experimental configuration was created to allow for more-accurate characterization of the spontaneous Raman scattering properties in anisotropic materials. This need stems from the challenges, arising from the complexity of light propagation, in obtaining accurate measurements of the angular dependence of the Raman scattering cross section in birefringent materials. The nonlinear optical material KH 2 PO 4 (KDP) is used as a model medium. Our report is motivated by the need to improve our understanding and management of transverse stimulated Raman scattering in KDP crystals and its deuterated analog, DKDP, typically used for frequency conversion and polarization control in large-aperture laser systems. Key to this experimental platform is the use of high-quality spherical samples that enable one to measure the Raman scattering cross section in a wide range of geometries using only a single sample. The effect of polarization rotation of both the pump light and the collected Raman signal must be carefully considered in data analysis and can give rise to artifacts, which can, in part, be mitigated by reducing the input and collection cone angles.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Structural Characterization of Alzheimer DNA Promoter Sequences from the Amyloid Precursor Gene in the Presence of Thioflavin T and Analogs

Understanding DNA-ligand binding interactions requires ligand screening, crystallization, and structure determination. In order to obtain insights into the amyloid peptide precursor (APP) gene-Thioflavin T (ThT) interaction, single crystals of two DNA sequences 5'-GCCCACCACGGC-3' (PDB 8ASK) and d(CCGGGGTACCCCGG) 2 (PDB 8ASH) were grown in the presence of ThT or its analogue 2-((4-(dimethylamino)benzylidene)amino)-3,6-dimethylbenzo[d]thiazol-3-ium iodide (XRB). Both structures were solved by molecular replacement. In the case of 8ASK, the space group was H3 with unit cell dimensions of a = b = 64.49 Å, c = 46.19 Å. Phases were obtained using a model generated by X3DNA. The novel 12-base-pair B-DNA structure did not have extra density for the ThT ligand. The 14-base-pair A-DNA structure with bound ThT analog XRB was isomorphous with previously the obtained apo-DNA structure 5WV7 (space group was P 4 1 2 1 2 with unit cell dimensions a = b = 41.76 Å, c = 88.96 Å). Binding of XRB to DNA slightly changes the DNA's buckle parameters at the CpG regions. Comparison of the two conformations of the XRB molecule: alone and bound to DNA indicates that the binding results from the freedom of rotation of the two aromatic rings.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

High-Speed and High-Power Ferroelectric Switching Current Measurement Instrument for Materials with Large Coercive Voltage and Remanent Polarization

A high-speed and high-power current measurement instrument is described for measuring rapid switching of ferroelectric samples with large spontaneous polarization and coercive field. Instrument capabilities (±200 V, 200 mA, and 200 ns order response) are validated with a LiTaO 3 single crystal whose switching kinetics are well known. The new instrument described here enables measurements that are not possible using existing commercial measurement systems, including the observation of ferroelectric switching in large coercive field and large spontaneous polarization Al 0.7 Sc 0.3 N thin films.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2021

Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP

YiiP is a secondary transporter that couples Zn 2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn 2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn 2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn 2+ . To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn 2+ and validated its performance with known Zn 2+ -binding proteins. Using these tools, we find that, in the presence of Zn 2+ , YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn 2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn 2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn 2+ binding sites and their role in the conformational dynamics that govern the transport cycle.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Tuning anisotropic bonding via chemistry and pressure in layered pnictides and chalcogenides (Final Report)

The overarching goal of this research program, as originally delineated in the proposal “Tuning anisotropic bonding via chemistry and pressure in layered pnictides and chalcogenides” was to develop a predictive, chemistry-driven understanding of the impact of the phonon behavior on thermal properties of bulk layered materials. At finite temperatures, atomic vibrations (phonons) strongly impact the thermodynamics, thermal and electrical transport, and phase-switching properties of functional materials. In particular, soft phonon modes and strongly anharmonic potentials can have spectacular consequences, including structural phase transitions (for example in ferroelectrics and phase-change memory materials), metal-insulator transitions, and extreme thermal resistance preventing heat propagation. Bulk materials with highly-anisotropic bonding may provide unique strategies to induce soft-phonon modes and lattice instabilities. Recently, increasingly detailed investigations of the lattice dynamics in layered materials have been made possible by the advent of first-principles phonon calculations and advanced characterization techniques based on neutron and X-ray scattering. However, due to the lack of studies in which composition and bonding character are systematically varied, there are still fundamental questions regarding the impacts of anisotropic bonding and anharmonicity on lattice stability and thermal transport. One of the major goals of this research program is therefore to address this gap by coherently tuning bonding anisotropy and anharmonicity across families of related compounds. Such approaches have revealed new strategies for exploiting structural anisotropy in quasi-1D and 2D bulk materials to obtain tailored functional properties. This project systematically explored the lattice dynamics, phase stability, and transport properties in bulk layered materials by using both composition and applied pressure to tune the degree of bonding anisotropy and anharmonicity. To accomplish this work, we combined i) single-crystal growth of key material systems with tunable anisotropy, ii) in-situ high-temperature/high-pressure characterization of structure and phonons to probe bonding anisotropy and anharmonicity, including state-of-the-art inelastic X-ray scattering (IXS) and inelastic neutron scattering (INS), and iii) first-principles simulations leveraging large-scale computing to identify the fundamental origins of the observed effects, by relating atomic structure and dynamics to electronic orbital interactions. Finally, we modeled and verified the impact of the phonon behavior on thermal transport to identify new strategies for a-priori design of thermal conductivity. Our integrated collaborative approach helped to systematically unravel the effects of anisotropy and bonding anharmonicity on phonon transport, thermodynamics, and thermal properties of complex anisotropic materials.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2022

Tuning anisotropic bonding via chemistry and pressure in layered pnictides and chalcogenides. Final Report

36 MATERIALS SCIENCE↗

DOE OSTI2021

Single-Particle Studies Reveal a Nanoscale Mechanism for Elastic, Bright, and Repeatable ZnS:Mn Mechanoluminescence in a Low-Pressure Regime

Mechanoluminescent materials, which emit light in response to elastic deformation, are demanded for use as in situ stress sensors. ZnS doped with Mn is known to exhibit one of the lowest reported thresholds for appearance of mechanoluminescence, with repeatable light emission under contact pressure <10 MPa. Here, the physical basis for such behavior remains as yet unclear. Here, reliable microscopic detection of mechanoluminescence of single ZnS:Mn microparticles, in combination with nanoscale structural characterization, provides evidence that the mechanoluminescent properties of these particles result from interplay between a non-centrosymmetric crystal lattice and its defects, viz., dislocations and stacking faults. Statistical analysis of the distributions of mechanoluminescence energy release trajectories reveals two distinct mechanisms of excitation: one attributable to a piezo-phototronic effect and the other due to dislocation motion. At pressures below 8.1 MPa, both mechanisms contribute to mechanoluminescent output, with a dominant contribution from the piezo-phototronic mechanism. In contrast, above 8.1 MPa, dislocation motion is the primary excitation source. For the piezo-phototronic mechanism, we propose a specific model that accounts for elastic ZnS:Mn mechanoluminescence under very low pressure. The charged interfaces in stacking faults lead to the presence of filled traps, which otherwise would be empty in the absence of the built-in electric field. Upon application of external stress, local enhancement of the piezoelectric field at the stacking faults’ interfaces facilitates release of the trapped carriers and subsequent luminescence. This field enhancement explains how <10 MPa pressure produces thousands of photons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

A Kinetic Model of the Long-Term Corrosion of Glass-Ceramic Materials

Multiphase waste forms show promise for increased waste loading and for the ability to dispose of contaminated solid and particulate waste through direct densification. However, achieving predictive capability for long-term durability of multiphase waste forms, and thus assessing their possible deployment, requires expanding the current, limited knowledge base. Here, we describe the development of a corrosion model of a two-phase waste form consisting of crystals of known volume fraction embedded in a glass matrix. This model accounts for the dissolution of both the crystalline and glass phases as well as the hydration of the glass phase through an ion exchange reaction. Because of the large difference in solubility between the two phases, the reactive surface of the crystalline phase is a function of the extent of dissolution of the glass phase in this model. Model parameterization was performed using corrosion data, such as from single-pass flow-through tests, for the individual phases. The parameterized corrosion model was evaluated against static dissolution test data for a glass-ceramic multiphase waste form. This evaluation demonstrated the model’s ability to reproduce the time-dependent release of key tracers of glass and crystalline phase dissolution. Hence, the development of a kinetic model provides a pathway for long-term durability predictions and thus the use of multiphase waste forms in nuclear cleanup missions.

Kerisit, Sebastien N.↗

DOE OSTI2024

Venturing into Unexplored Phase Space: Synthesis, Structure, and Properties of MgCo 3 B 2 Featuring a Rumpled Kagomé Network

MgCo 3 B 2 , a novel ternary boride in a previously unexplored phase space, was synthesized using the hydride route. In situ powder X-ray diffraction and DFT calculations aided in the discovery of this compound, whose structure was then determined by single-crystal X-ray diffraction. Like the closely related CeCo 3 B 2 , MgCo 3 B 2 crystallizes in centrosymmetric space group P6/mmm (a = 4.883(2) Å, c = 2.926(2) Å at 210 K, Z = 1). Unlike CeCo 3 B 2 , however, it adopts a disordered structure that features a rumpled Kagomé network of Co atoms, and Mg atoms fill the channels of a Co–B framework. Although the structural disorder leads to motifs that are similar to those observed in MgNi 3 B 2 and other related ternary borides, no evidence of an ordered superstructure was found by single-crystal X-ray diffraction or high-resolution powder X-ray diffraction. In the case of CeCo 3 B 2 , boron atoms occupy the center of regular Co 6 trigonal prisms; in MgCo 3 B 2 , boron atoms are shifted from the center of the prism to form B–B dimers with roughly the same length as those found in MgNi 3 B 2 . Magnetic susceptibility data exhibit an unusual temperature dependence that cannot be convincingly modeled by the modified Curie–Weiss equation, consistent with DFT calculations predicting a nonmagnetic ground state. Intrinsic susceptibility at 300 K is 1.42 × 10 –3 emu/mol Oe, which is comparable to that of paramagnetic YCo 3 B 2 and CeCo 3 B 2 with a similar structure and composition. Here, this study showcases the efficacy of combining several methodologies to discover new solids in unexplored phase spaces. This approach includes in situ PXRD data to monitor reactions of precursors upon heating, a diffusion-enhanced synthesis method, and DFT assessment of compound stability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Enhanced Electrocatalytic and Selective CO 2 -to-CO Reduction by a Rhenium(I) Complex Bearing 6,6′-Substituted 2,2′-Bipyridines

The electrochemical reduction of CO 2 (CO 2 RR) into value-added chemicals offers a promising route toward a circular carbon economy and reduced reliance on fossil fuels. A detailed understanding of the structural and electronic factors governing the performance of molecular CO 2 RR electrocatalysts is essential for the design of efficient, tunable systems. Here, in this study, we report a series of rhenium(I) complexes, fac-[Re I (6,6′-(R) 2 -bpy)(CO) 3 Cl] (bpy = 2,2′-bipyridine; R = mesityl (mes), 2,4,6-triisopropylphenyl (trip), or isophthalic acid (phth)) and evaluate their electrocatalytic activity. Among these, fac-[Re I (6,6′-(mes) 2 -bpy)(CO) 3 Cl] exhibited the highest performance, enabling selective CO 2 -to-CO conversion for 1 hour with Faradaic efficiency (FE) > 97%, representing an unprecedented activity level for a Re-bpy catalysts. Single-crystal X-ray diffraction and density functional theory (DFT) calculations indicated that favorable CO 2 binding could be promoted by the tilting of the 6,6′-(mes)2-bpy ligand (from the Re-CO coordination plane), providing mechanistic insight into the observed enhancement. The study consequently demonstrates a rational correlation between the CO 2 electrocatalytic performance of Re-bpy catalysts and their structural variations, as derived from X-ray data and corroborated by computational modeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Hallucination of closed repeat proteins containing central pockets

In pseudocyclic proteins, such as TIM barrels, β barrels, and some helical transmembrane channels, a single subunit is repeated in a cyclic pattern, giving rise to a central cavity that can serve as a pocket for ligand binding or enzymatic activity. Inspired by these proteins, we devised a deep-learning-based approach to broadly exploring the space of closed repeat proteins starting from only a specification of the repeat number and length. Biophysical data for 38 structurally diverse pseudocyclic designs produced in Escherichia coli are consistent with the design models, and the three crystal structures we were able to obtain are very close to the designed structures. Docking studies suggest the diversity of folds and central pockets provide effective starting points for designing small-molecule binders and enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Quantitative investigation of surface structure and interatomic potential with impact-collision ion scattering spectroscopy

Helium ion beam interactions with materials have important implications for magnetic confinement fusion, material modification, and helium ion microscopy. These interactions depend on the precise physics of how helium ions channel into the materials, which can vary greatly based on the local crystalline orientation. Here, we performed a dedicated experiment to investigate helium ion channeling in a well-characterized tungsten single crystal. Time-of-flight impact-collision ion scattering spectroscopy was used to obtain multi-angle maps of the backscattering intensity for 3 keV He + → W(111). We found that the backscattering intensity profile arising from helium ion channeling could be well described by a shadow cone analysis. This analysis revealed that subsurface W atoms as deep as the ninth monolayer contributed to the backscattering intensity profile. Binary collision approximation simulations were performed with MARLOWE to model the experimental maps with sufficient accuracy to allow for quantitative comparisons using reliability factors. These quantitative comparisons were applied to investigate how the W lattice structure and He–W interatomic potential affect the multi-angle maps.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

Non-conformal interface-cohesive modeling with the shifted boundary method

The accurate simulation of boundary- and interface-dominated problems on complex geometries remains challenging when boundary- or interface-fitted meshes are difficult to generate, particularly for curved boundaries, polycrystalline microstructures, and dense interface networks. The Shifted Boundary Method (SBM) alleviates this meshing burden by shifting the enforcement of boundary conditions from the true boundary to a nearby surrogate boundary and recovering the effect of the true boundary through geometric correction terms, thereby enabling standard finite element spaces on non-boundary-fitted meshes. In this report, we develop a general shiftedboundary and shifted-interface framework within the open-source MOOSE framework. We first present a general SBM implementation for complex geometries on non-boundary-fitted meshes. We then adopt the Shifted Interface Method (SIM) for internal interfaces and develop a unified shifted-interface treatment in which the interface law is enforced on a surrogate interface and the effect of the true interface is recovered through shifted jumps, fluxes, and tractions. This perspective brings scalar thermal-contact and vector-valued cohesive-zone mechanics into a single framework, the latter realized as the Shifted Cohesive Zone Method (SCZM) and coupled with history-dependent constitutive models from NEML2. We further extend the MOOSE mesh infrastructure to support cohesive-zone calculations on distributed meshes. The framework is verified and demonstrated through three progressive studies: Poisson’s equation on a smoothed starshaped domain, a manufactured thermal-contact problem on a non-interface-fitted mesh, and a two-dimensional polycrystalline representative volume element combining crystal plasticity with cohesive grain-boundary interfaces. Across these studies, the shifted formulations reproduce boundary- and interface-fitted reference solutions with high fidelity, indicating that the proposed framework provides an accurate and efficient route to boundary- and interface-dominated simulations on arbitrary geometries without requiring fitted meshes.

Yang, Cheng-Hau↗