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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.

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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Abstract Motivation The state-of-art protein structure prediction methods such as AlphaFold are being widely used to predict structures of uncharacterized proteins in biomedical research. There is a significant need to further improve the quality and nativeness of the predicted structures to enhance their usability. In this work, we develop ATOMRefine, a deep learning-based, end-to-end, all-atom protein structural model refinement method. It uses a SE(3)-equivariant graph transformer network to directly refine protein atomic coordinates in a predicted tertiary structure represented as a molecular graph. Results The method is first trained and tested on the structural models in AlphaFoldDB whose experimental structures are known, and then blindly tested on 69 CASP14 regular targets and 7 CASP14 refinement targets. ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial structural models generated by AlphaFold. It also performs better than two state-of-the-art refinement methods in multiple evaluation metrics including an all-atom model quality score—the MolProbity score based on the analysis of all-atom contacts, bond length, atom clashes, torsion angles, and side-chain rotamers. As ATOMRefine can refine a protein structure quickly, it provides a viable, fast solution for improving protein geometry and fixing structural errors of predicted structures through direct coordinate refinement. Availability and implementation The source code of ATOMRefine is available in the GitHub repository (https://github.com/BioinfoMachineLearning/ATOMRefine). All the required data for training and testing are available at https://doi.org/10.5281/zenodo.6944368.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Site-Selective Polyolefin Hydrogenolysis on Atomic Ru for Methanation Suppression and Liquid Fuel Production

Catalytic hydrogenolysis of end-of-life polyolefins can produce value-added liquid fuels and therefore holds great promises in plastic waste reuse and environmental remediation. The major challenge limiting the recycling economic benefit is the severe methanation (usually >20%) induced by terminal C–C cleavage and fragmentation in polyolefin chains. Here, we overcome this challenge by demonstrating that Ru single-atom catalyst can effectively suppress methanation by inhibiting terminal C–C cleavage and preventing chain fragmentation that typically occurs on multi-Ru sites. The Ru single-atom catalyst supported on CeO 2 shows an ultralow CH 4 yield of 2.2% and a liquid fuel yield of over 94.5% with a production rate of 314.93 g fuels g Ru -1 h -1 at 250 °C for 6 h. Such remarkable catalytic activity and selectivity of Ru single-atom catalyst in polyolefin hydrogenolysis offer immense opportunities for plastic upcycling.

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

Fluorinated ionic liquids for battery electrolytes

An ionic liquid comprising a cationic chemical species and an anionic chemical species. The cationic chemical species comprising a nitrogen containing moiety and a partially fluorinated alkyl chain moiety, wherein the partially fluorinated alkyl chain moiety is bonded to a nitrogen atom of the nitrogen containing moiety. The ionic liquid can be used as an electrolyte, as an additive to an organic solvent, as a lubricant, as a hydrophobic coating, as a treatment for fluorinated pollutants, as an electrolyte for sensor applications, as a stabilizing additive for existing battery electrolytes, and as an emulsifier.

25 ENERGY STORAGE↗
DOE OSTI2020

MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids

Peptoids (poly-N-substituted glycines) are a class of synthetic polymers that are regioisomers of peptides (poly-C-substituted glycines), in which the point of side-chain connectivity is shifted from the backbone C to the N atom. Peptoids have found diverse applications as peptidomimetic drugs, protein mimetic polymers, surfactants, and catalysts. Computational modeling is valuable in the understanding and design of peptoid-based nanomaterials. In this work, we report the bottom-up parameterization of coarse-grained peptoid force fields based on the MARTINI peptide force field against all-atom peptoid simulation data. Our parameterization pipeline iteratively refits coarse-grained bonded interactions using iterative Boltzmann inversion and nonbonded interactions by matching the potential of mean force for chain extension. We assure good sampling of the amide bond cis/trans isomerizations in the all-atom simulation data using parallel bias metadynamics. We develop coarse-grained models for two representative peptoids—polysarcosine (poly(N-methyl glycine)) and poly(N-((4-bromophenyl)ethyl)glycine)—and show their structural and thermodynamic properties to be in excellent accord with all-atom calculations but up to 25-fold more efficient and compatible with MARTINI force fields. Here, this work establishes a new rigorously parameterized coarse-grained peptoid force field for the understanding and design of peptoid nanomaterials at length and time scales inaccessible to all-atom calculations.

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

Side Chain Regioisomers that Dictate Optical Properties and Mechanofluorochromism through Crystal Packing

Designing strong interactions into $π$-conjugated materials can direct their typically uncontrolled molecular packing and is an important strategy toward tuning their technologically relevant properties in the solid state. In this paper we demonstrate unconventional control over solid-state fluorescence and mechanofluorochromism (MFC) through regiochemical substitutions in side chains of 12 three-ring phenylene ethynylenes (PEs) that employ fluoroarene–arene (ArF–ArH) interactions between tetrafluoro ArF pendants and PE main chains to direct crystal packing, with single-atom variations of the lone proton in ArF pendants between 4-hydro, 5-hydro, and 6-hydro substitution yielding in two cases dramatically different fluorescence and MFC behavior. X-ray crystal structures reveal key intermolecular interactions of ArF rings, including their lone protons, which vary as a function of substitution pattern and contribute to optical properties in solids. Rarely reported, particularly with such dramatic results, this systematic study on regiochemical effects over solid-state properties demonstrates the versatility of using discrete, directional interactions of side chains for noncovalent control in conjugated materials.

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

Controlling quantum many-body dynamics in driven Rydberg atom arrays

Dynamic stabilization of an array Large-scale systems comprising one-dimensional chains and two-dimensional arrays of excited atoms held in a programmable optical lattice are a powerful platform with which to simulate emergent phenomena. Bluvstein et al. built an array of up to 200 Rydberg atoms and subjected the system to periodic excitation. Under such driven excitation, they found that the array of atoms stabilized, freezing periodically into what looked like time crystals. Understanding and controlling the dynamic interactions in quantum many-body systems lies at the heart of contemporary condensed matter physics and the exotic phenomena that can occur. Science , this issue p. 1355

Science & Technology - Other Topics↗
DOE OSTI2024

Evidence of short chains in liquid sulfur

High energy x-ray pair distribution function measurements show the average coordination number of the first shell in liquid sulfur is 1.86 ± 0.04 across the λ-transition, not precisely 2.0 as widely accepted. This indicates that upon melting, liquid sulfur does not comprise solely of S 8 rings but also possesses a significant number of short chains. Intensities of the pre-peak and first diffraction peak of the x-ray structure factor and third peak height of the pair distribution function all show deviations at the λ-transition temperature T λ , associated with the break-up of S 8 rings and the start of oligomer polymerization. A significant number of non-bonded or loosely bonded “interstitial atoms,” with an average coordination number of 0.20 ± 0.005, are also observed in the so-called “forbidden zone” between the first and second shells upon melting. The number of interstitial atoms is found to decrease to a minimum at the λ-transition, but the majority persist into the high temperature polymerized liquid. Furthermore, the existence of short chains and nearby interstitial atoms represent the two main factors required to initiate the S 8 -ring to chain transition, as proposed by recent molecular dynamics simulations.

Chemical bonding↗
DOE OSTI2020

Stabilization of NbTe 3 , VTe 3 , and TiTe 3 via Nanotube Encapsulation

The structure of MX 3 transition metal trichalcogenides (TMTs, with M a transition metal and X a chalcogen) is typified by one-dimensional (1D) chains weakly bound together via van der Waals interactions. This structural motif is common across a range of M and X atoms (e.g. NbSe 3 , HfTe 3 , TaS 3 ), but not all M and X combinations are stable. We report here that three new members of the MX 3 family which are not stable in bulk, specifically NbTe 3 , VTe 3 , and TiTe 3 , can be synthesized in the few- to single-chain limit via nano-confined growth within the stabilizing cavity of multi-walled carbon nanotubes. Transmission electron microscopy (TEM) and atomic-resolution scanning transmission electron microscopy (STEM) reveal the chain-like nature and the detailed atomic structure. The synthesized materials exhibit behavior unique to few-chain quasi-1D structures, such as multi-chain spiraling and a trigonal anti-prismatic rocking distortion in the single-chain limit. Density functional theory (DFT) calculations provide insight into the crystal structure and stability of the materials, as well as their electronic structure.

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

DOE Challenges and Opportunities Associated with Accountable Nuclear Material Needs for Development and Commercialization of Fusion Nuclear Energy

Fusion energy represents a transformative opportunity to deliver a safe, plentiful, and carbon-free source of reliable primary power. In recent years, fusion research and development have accelerated significantly, particularly within the US, driven by decades of foundational public investment. Notably, in 2024 the US Department of Energy (DOE) established a comprehensive Fusion Energy Strategy aimed at collaborating with industry partners to enable the deployment of fusion power plants and grid integration by the 2030s. This strategy is chiefly implemented through the DOE Office of Science (SC) Fusion Energy Sciences program. This project was initiated to identify potential approaches for the Office of Environment, Safety, and Health (NA-ESH-12) within DOE’s National Nuclear Security Administration to begin engagement with the fusion community on future accountable material needs. The goal of the project is to inform and influence the supply of and demand for accountable nuclear materials as fusion energy is developed and commercialized. NA-ESH-12 must proactively engage with the fusion community regarding the production and management of accountable nuclear materials. Given the complexity and scale of materials required for research, pilot projects, and eventual commercial reactors, early coordination is vital. The project’s objective is to provide insights that will shape the supply and demand landscape for critical nuclear materials, ensuring that DOE is prepared to effectively support fusion energy development and commercialization. In FY 2025, an initial limited review was conducted to identify the status of the fusion energy community’s progress toward full-scale energy production and the need for accountable nuclear material. This included communications with SC, NA-ESH-12, Savannah River National Laboratory, and Oak Ridge National Laboratory, and attending the Rutgers University–sponsored Supply Chain Workshop: Scaling the Fusion Industry and the International Atomic Energy Agency’s Ninth DEMO Programme Workshop. The review to date indicates that the amounts of tritium, lithium-6, and deuterium required by the fusion industry will be dependent on fuel type, breeding technology, blankets, and R&D improvements. One concern is that the commercial sector does not have a sufficient supply chain to meet the demand for development and commercialization for fusion energy production. The supply and demand estimates for these materials should be routinely reviewed as fusion technologies mature.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Radical Borylation of Alkyl Bromides by Photoinduced Halogen‐Atom Transfer

Alkyl organoboron compounds are versatile synthons in organic synthesis, enabling rapid access to a variety of carbon─carbon and carbon-heteroatom bonds. As such, strategies to efficiently access carbon-boron bonds from simple chemical feedstocks are highly desirable. The radical borylation of alkyl bromides presents an attractive approach. However, the activation of alkyl bromides typically requires strong reductants or transition-metal catalysts. Herein, we report a metal-free radical borylation strategy of various alkyl bromides utilizing a photoinduced silyl radical to mediate a halogen-atom transfer process. This method demonstrates broad utility and functional group tolerance among various primary, secondary, and tertiary unactivated alkyl bromides and can facilitate the functionalization of pharmaceutically relevant motifs. Mechanistic and computational studies support a radical-chain pathway involving a silyl radical-mediated halogen-atom transfer.

Alkyls↗
DOE OSTI2020

Evidence that Criegee intermediates drive autoxidation in unsaturated lipids

Significance Autoxidation leads to the slow persistent destruction of organic molecules causing oxidative stress and associated disease. The prevailing autoxidation mechanism of unsaturated lipids involves chain reactions initiated and propagated by H-atom abstraction, mediated by peroxy radicals and other reactive oxygen species. Here we report experimental evidence for an autoxidation mechanism initiated by OH, which is unanticipated and proceeds by OH addition followed by pathways involving Criegee intermediates (CIs). Although CIs are routinely encountered in atmospheric and synthetic organic chemistry, their role in autoxidation is unexpected. Our results suggest that in all likelihood these exotic species play a much more prominent and general role in the chemistry of cells, food, petrochemicals, and the environment beyond what is currently believed.

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

One-dimensionality signature in optical conductivity of heavy-fermion CeIr 3 B 2

In low dimensions, the combined effects of interactions and quantum fluctuations can lead to dramatically new physics distinct from that existing in higher dimensions. Here, we investigate the electronic and optical properties of CeIr 3 ⁢B 2 , a quasione-dimensional (1D) Kondo lattice system, using ab initio calculations. The Ce atoms in the hexagonal crystal structure form 1D chains along the c axis, with extremely short Ce-Ce distances. The quasi-1D nature of the crystal structure is well reflected in its electronic structure. Extremely flat bands emerge within the ab plane of the Brillouin zone, yielding sharp optical transitions in the corresponding optical conductivity. Further, our calculations indicate that these prominent peaks in the optical conductivity provide a clear signature of quasi-1D heavy fermion systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Dynamics of nonequilibrium magnons in gapped Heisenberg antiferromagnets

Nonequilibrium dynamics in spin systems is a topic currently under intense investigation as it provides fundamental insights into thermalization, universality, and exotic transport phenomena. While most of the studies have been focused on ideal closed quantum many-body systems such as ultracold atomic quantum gases and one-dimensional spin chains, driven-dissipative Bose gases in steady states away from equilibrium in classical systems also lead to intriguing nonequilibrium physics. Here, in this work, we theoretically investigate out-of-equilibrium dynamics of magnons in a gapped Heisenberg quantum antiferromagnet based on Boltzmann transport theory. We show that, by treating scattering terms beyond the relaxation-time approximation in the Boltzmann transport equation, energy and particle number conservation mandate that nonequilibrium magnons cannot relax to equilibrium, but decay to other nonequilibrium stationary states. The only decay channel for these stationary states back to equilibrium is through the nonconserving interactions (i.e., changing particle number and/or energy within the magnon system) such as boundary or magnon-phonon scattering. At low temperatures, these nonconserving interactions are much slower processes than intrinsic magnon-magnon interaction in a gapped spin system. Using magnon-phonon interaction as a quintessential type of nonconserving interaction, we then propose that nonequilibrium steady states of magnons can be maintained and tailored using periodic driving at frequencies faster than relaxation due to phonon interactions. These findings reveal a class of classical material systems that are suitable platforms to study nonequilibrium statistical physics and macroscopic phenomena such as classical Bose-Einstein condensation of quasiparticles and magnon supercurrents that are relevant for spintronic applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Chicago Pile-1 paved the way for nuclear science and a lab in Los Alamos First self-sustaining nuclear chain reaction was nearly 80 years ago

On a bitter-cold winter day, 43 scientists gathered at an abandoned squash court at the University of Chicago where they would ultimately enable a secret lab in Los Alamos to change the world just years later. It was December 2, 1942. The group, led by Italian physicist and Nobel laureate Enrico Fermi, stacked graphite bricks, piling 57 layers that totaled more than 770,000 pounds. Later named Chicago Pile-1, their goal was to create the world’s first self-sustaining, controlled nuclear chain reaction. Inside the approximately 20-feet-tall pile were smaller blocks of uranium and control rods that, when removed, would cause the reaction to go critical – meaning create a nuclear chain reaction. It was roughly $1 million worth of materials, equivalent to nearly $16 million today, and a concept that a nuclear chain reaction would allow the weaponization of the atom. “Its success would be the crucial proof needed to know it would be possible to create an atomic bomb,” said LANL Historian Roger Meade (C-NR). “This was the precursor to the Lab we have today, nearly 80 years later.”

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

XFEL Microcrystallography of Self-Assembling Silver n -Alkanethiolates

New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd–even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd–even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd–even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. Finally, we conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Atomic-Scale Imaging Reveals Polar-π Interactions in Two-Dimensional Molecular Superlattices

Controlling coassembly of synthetic oligomers into binary superlattices at the atomic level is challenging. Here, we report a strategy for programming polar-π interactions in oligomeric peptoids, a class of sequence-defined peptidomimetics, facilitating the formation of homogeneous two-dimensional (2D) superlattices. N-2-phenylethyl and N-(2-perfluorophenyl)ethyl side chains, similar in size, but with contrasting electrostatic characteristics, were introduced at defined sequence positions to generate favorable dipolar aromatic interactions. The resulting nanosheets exhibit different crystal motifs depending on the side chain interactions: systems containing only one type of aromatic side chain form a parallel V-shaped motif driven by π-π interactions, whereas a combination of both types of aromatic side chains, either within one backbone or through the coassembly of two distinct peptoids, adopt an antiparallel V-shaped superlattice with higher thermal stability, driven by polar-π interactions. Cryogenic transmission electron microscopy directly resolved the packing arrangement of perfluorophenyl and phenyl rings in individual nanosheet superlattices, confirming that intermolecular polar-π interaction dominates the superlattice motifs and increases lattice stability. Molecular dynamics simulations and density functional theory calculations further substantiate the energetic favorability of polar-π interactions over π-π interactions, rationalizing the formation of homogeneous superlattices with enhanced thermal stability. Our discoveries establish a design principle for binary coassembly using sequence-defined oligomers, which enables control over unit cell geometry, lattice stability, and molecular registration through aromatic side chain polarization and sequence control. This ability to program atomic-scale binary superlattices opens new avenues for designing functional 2D soft materials.

Lee, Yen Jea [Lawrence Berkeley National Laborator↗
DOE OSTI2025

Internally Catalyzed Hydrogen Atom Transfer (I-CHAT)—A New Class of Reactions in Combustion Chemistry

The current paradigm of low-T combustion and autoignition of hydrocarbons is based on the sequential two-step oxygenation of fuel radicals. The key chain-branching occurs when the second oxygenation adduct (OOQOOH) is isomerized releasing an OH radical and a key ketohydroperoxide (KHP) intermediate. The subsequent homolytic dissociation of relatively weak O–O bonds in KHP generates two more radicals in the oxidation chain leading to ignition. Based on the recently introduced intramolecular “catalytic hydrogen atom transfer” mechanism (J. Phys. Chem. 2024, 128, 2169), abbreviated here as I-CHAT, we have identified a novel unimolecular decomposition channel for KHPs to form their classical isomers—enol hydroperoxides (EHP). The uncertainty in the contribution of enols is typically due to the high computed barriers for conventional (“direct”) keto–enol tautomerization. Remarkably, the I-CHAT dramatically reduces such barriers. The novel mechanism can be regarded as an intramolecular version of the intermolecular relay transfer of H-atoms mediated by an external molecule following the general classification of such processes (Catal. Rev.-Sci. Eng. 2014, 56, 403). Here, we present a detailed mechanistic and kinetic analysis of the I-CHAT-facilitated pathways applied to n-hexane, n-heptane, and n-pentane models as prototype molecules for gasoline, diesel, and hybrid rocket fuels. We particularly examined the formation kinetics and subsequent dissociation of the γ-enol-hydroperoxide isomer of the most abundant pentane-derived isomer γ-C5-KHP observed experimentally. To gain molecular-level insight into the I-CHAT catalysis, we have also explored the role of the internal catalyst moieties using truncated models. All applied models demonstrated a significant reduction in the isomerization barriers, primarily due to the decreased ring strain in transition states. In addition, the longer-range and sequential H-migration processes were also identified and illustrated via a combined double keto–enol conversion of heptane-2,6-diketo-4-hydroperoxide as a potential chain-branching model. To assess the possible impact of the I-CHAT channels on global fuel combustion characteristics, we performed a detailed kinetic analysis of the isomerization and decomposition of γ-C5-KHP comparing I-CHAT with key alternative reactions—direct dissociation and Korcek channels. Calculated rate parameters were implemented into a modified version of the n-pentane kinetic model developed earlier using RMG automated model generation tools (ACS Omega, 2023, 8, 4908). Simulations of ignition delay times revealed the significant effect of the new pathways, suggesting an important role of the I-CHAT pathways in the low-T combustion of large alkanes.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Direct Observation of Twin van der Waals Molecular Chains

The van der Waals (vdW) assemblies are the most common structures of materials. However, directly mapping intermolecular electron clouds of a vdW assembly has never been obtained, even though the intramolecular electron clouds were visualized by atomic-resolution techniques. In this report, we unprecedently mapped the intermolecular electron cloud of the assembles of ethanol molecules via ethyl groups with noncontact atomic force microscopy at 5 K, leading to the first visualization of vdW molecular chains, in which ethanol molecules assemble into twin vdW molecular chains in a reverse parallel configuration on Ag(111) plane. Furthermore, spontaneous order-disorder transitions in the chain were dynamically observed, suggesting its unusual properties different from 2D vdW materials. In conclusion, these findings provide an "eye" to see the atomic world of vdW materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗