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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Experimental and Computational Evaluation of Lipidomic In-Source Fragmentation as a Result of Postionization with Matrix-Assisted Laser Desorption/Ionization

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) can provide spatially resolved molecular information about a sample. Recently, a postionization approach (MALDI-2) has been commercially integrated with MALDI-MSI, allowing for bettered sensitivity and consequent improved spatial resolution. While advantages of MALDI-2 have previously been established, we demonstrate here statistically increased in-source fragmentation (ISF) results from postionization with a commercial instrument. Via lipid standard analyses, known MALDI ISF pathways (e.g., loss of trimethylamine) were statistically increased in MALDI-2 compared to MALDI-1 (65–172% increase in fragmentation). Gas phase molecular modeling with density functional theory estimated that the most-weighted virtual orbitals to excite within lipids involve ester and phosphate bonds. Protonated lipid excitation energies are furthermore red-shifted compared to those of other adduct types [e.g., 254 nm for protonated PC(16:0/18:1)] and approach the MALDI-2 laser energy (266 nm). Analysis of rat brain homogenate detected statistically more positive-ion mode peaks with MALDI-2 (1090) than that with MALDI-1 (719), where Kernel density estimations showed that the majority of this enhancement occurs with low m/z ions (i.e., m/z 75–500). Taken together with the lipid standard data, these observations may indicate ISF due to postionization. Finally, while artifact contributions from matrix blanks were also noted, both experimental and computational data sets suggest that the overall extent of ISF is statistically increased in MALDI-2 compared to MALDI-1.

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

Computational and Experimental Determination of the Properties, Structure, and Stability of Peptoid Nanosheets and Nanotubes

Peptoids (N-substituted glycines) are a group of highly controllable peptidomimetic polymers. Amphiphilic diblock peptoids have been engineered to assemble crystalline nanospheres, nanofibrils, nanosheets, and nanotubes with biochemical, biomedical, and bioengineering applications. The mechanical properties of peptoid nanoaggregates and their relationship to the emergent self-assembled morphologies have been relatively unexplored and are critical for the rational design of peptoid nanomaterials. In this work, we consider a family of amphiphilic diblock peptoids consisting of a prototypical tube-former (Nbrpm6Nc6, a NH 2 -capped hydrophobic block of six N-((4-bromophenyl)methyl)glycine residues conjugated to a polar NH 3 (CH 2 ) 5 CO tail), a prototypical sheet-former (Nbrpe6Nc6, where the hydrophobic block comprises six N-((4-bromophenyl)ethyl)glycine residues), and an intermediate sequence that forms mixed structures ((NbrpeNbrpm)3Nc6). We combine all-atom molecular dynamics simulations and atomic force microscopy to determine the mechanical properties of the self-assembled 2D crystalline nanosheets and relate these properties to the observed self-assembled morphologies. We find good agreement between our computational predictions and experimental measurements of Young’s modulus of crystalline nanosheets. A computational analysis of the bending modulus along the two axes of the planar crystalline nanosheets reveals bending to be more favorable along the axis in which the peptoids stack by interdigitation of the side chains compared to that in which they form columnar crystals with π-stacked side chains. Here, we construct molecular models of nanotubes of the Nbrpm6Nc6 tube-forming peptoid and predict a stability optimum in good agreement with experimental measurements. A theoretical model of nanotube stability suggests that this optimum is a free energy minimum corresponding to a “Goldilocks” tube radius at which capillary wave fluctuations in the tube wall are minimized.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Computational Prediction of Coiled–Coil Protein Gelation Dynamics and Structure

Protein hydrogels represent an important and growing biomaterial for a multitude of applications, including diagnostics and drug delivery. We have previously explored the ability to engineer the thermoresponsive supramolecular assembly of coiled–coil proteins into hydrogels with varying gelation properties, where we have defined important parameters in the coiled–coil hydrogel design. Using Rosetta energy scores and Poisson–Boltzmann electrostatic energies, we iterate a computational design strategy to predict the gelation of coiled–coil proteins while simultaneously exploring five new coiled–coil protein hydrogel sequences. Provided this library, we explore the impact of in silico energies on structure and gelation kinetics, where we also reveal a range of blue autofluorescence that enables hydrogel disassembly and recovery. As a result of this library, we identify the new coiled–coil hydrogel sequence, Q5, capable of gelation within 24 h at 4 °C, a more than 2-fold increase over that of our previous iteration Q2. The fast gelation time of Q5 enables the assessment of structural transition in real time using small-angle X-ray scattering (SAXS) that is correlated to coarse-grained and atomistic molecular dynamics simulations revealing the supramolecular assembling behavior of coiled–coils toward nanofiber assembly and gelation. This work represents the first system of hydrogels with predictable self-assembly, autofluorescent capability, and a molecular model of coiled–coil fiber formation.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Oxide– and Silicate–Water Interfaces and Their Roles in Technology and the Environment

Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by “anomalies” or “non-idealities” such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide– and silicate–water interfaces. This critical review discusses how science progresses from understanding ideal solid–water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. Further, we anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration.

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

Theoretical and Experimental Advances in High-Pressure Behaviors of Nanoparticles

Using compressive mechanical forces, such as pressure, to induce crystallographic phase transitions and mesostructural changes while modulating material properties in nanoparticles (NPs) is a unique way to discover new phase behaviors, create novel nanostructures, and study emerging properties that are difficult to achieve under conventional conditions. In recent decades, NPs of a plethora of chemical compositions, sizes, shapes, surface ligands, and self-assembled mesostructures have been studied under pressure by in-situ scattering and/or spectroscopy techniques. As a result, the fundamental knowledge of pressure–structure–property relationships has been significantly improved, leading to a better understanding of the design guidelines for nanomaterial synthesis. In the present review, we discuss experimental progress in NP high-pressure research conducted primarily over roughly the past four years on semiconductor NPs, metal and metal oxide NPs, and perovskite NPs. We focus on the pressure-induced behaviors of NPs at both the atomic- and mesoscales, inorganic NP property changes upon compression, and the structural and property transitions of perovskite NPs under pressure. We further discuss in depth progress on molecular modeling, including simulations of ligand behavior, phase-change chalcogenides, layered transition metal dichalcogenides, boron nitride, and inorganic and hybrid organic–inorganic perovskites NPs. These models now provide both mechanistic explanations of experimental observations and predictive guidelines for future experimental design. Here, we conclude with a summary and our insights on future directions for exploration of nanomaterial phase transition, coupling, growth, and nanoelectronic and photonic properties.

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

Amidinate Supporting Ligands Influence Molecularity in Formation of Uranium Nitrides

Uranium nitride complexes are attractive targets for chemists as molecular models for the bonding, reactivity, and magnetic properties of next-generation nuclear fuels, but these molecules are uncommon and can be difficult to isolate due to their high reactivity. Here, we describe the synthesis of three new multinuclear uranium nitride complexes, [U(BCMA) 2 ] 2 (μ-N)(μ-κ 1 :κ 1 -BCMA) (7), [(U(BIMA) 2 ) 2 (μ-N)(μ-N i Pr)(K 2 (μ-η 3 :η 3 -CH 2 CHN i Pr)] 2 (8), and [U(BIMA) 2 ] 2 (μ-N)(μ-κ 1 :κ 1 -BIMA) (9) (BCMA = N,N-bis(cyclohexyl)methylamidinate, BIMA = N,N-bis(iso-propyl)methylamidinate), from U(III) and U(IV) amidinate precursors. By varying the amidinate ligand substituents and azide source, we were able to influence the composition and size of these nitride complexes. 15 N isotopic labeling experiments confirmed the bridging nitride moieties in 7–9 were formed via two-electron reduction of azide. The tetra-uranium cluster 8 was isolated in 99% yield via reductive cleavage of the amidinate ligands; this unusual molecule contains nitrogen-based ligands with formal 1–, 2–, and 3– charges. Additionally, chemical oxidation of the U(IV) precursor U(N 3 )(BCMA) 3 yielded the cationic U(V) species [U(N 3 )(BCMA) 3 ][OTf]. Magnetic susceptibility measurements confirmed a U(IV) oxidation state for the uranium centers in the three nitride-bridged complexes and provided a comparison of magnetic behavior in the structurally related U(III)-U(IV)-U(V) series U(BCMA) 3 , U(N 3 )(BCMA) 3 , and [U(N 3 )(BCMA) 3 ][OTf]. At 240 K, the magnetic moments in this series decreased with increasing oxidation state, i.e., U(III) > U(IV) > U(V); this trend follows the decreasing number of 5f valence electrons along this series.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

MOFX-DB: An Online Database of Computational Adsorption Data for Nanoporous Materials

Machine learning and data mining coupled with molecular modeling have become powerful tools for materials discovery. Metal-organic frameworks (MOFs) are a rich area for this due to their modular construction and numerous applications. Here, we make data from several previous large-scale studies in MOFs and zeolites from our groups (and new data for N 2 and Ar adsorption in MOFs) easily accessible in one place. The database includes over 3 million simulated adsorption data points for H 2 , CH 4 , CO 2 , Xe, Kr, Ar, and N 2 in over 160 000 MOFs and zeolites, textural properties like pore sizes and surface areas, and the structure file for each material. We include metadata about the Monte Carlo simulations to enable reproducibility. The database is searchable by MOF properties, and the data are stored in a standardized JSON format that that is interoperable with the NIST adsorption database. We also identify several MOFs that meet high performance targets for multiple applications, such as high storage capacity for both hydrogen and methane or high CO 2 capacity plus good Xe/Kr selectivity. Here, by providing this data publicly, we hope to facilitate machine learning studies on these materials, leading to new insights on adsorption in MOFs and zeolites.

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

Significance of Energy Conservation in Coupled-Trajectory Approaches to Nonadiabatic Dynamics

Practical methods for simulating photo-induced dynamics of molecules often rely on a trajectory-description of the nuclear dynamics, incorporating approximate electron-nuclear feedback. Through approximating electron–nuclear correlation terms in the exact factorization approach, trajectory-based methods have been derived and successfully applied to the dynamics of a variety of light-induced molecular processes, capturing quantum (de)coherence effects rigorously. These terms account for the coupling among the trajectories, recovering the nonlocal nature of quantum nuclear dynamics that is completely overlooked in traditional independent-trajectory algorithms. Nevertheless, some of the approximations introduced in the derivation of some of these methods do not conserve the total energy. We analyze energy conservation in the coupled trajectory mixed quantum-classical (CTMQC) algorithm and explore the performance of a modified algorithm, CTMQC-E, where some of the terms are redefined to restore energy conservation. Here, a set of molecular models is used as a test, namely, 2-cis-penta-2,4-dienimium cation, bis(methylene) adamantyl radical cation, butatriene cation, uracil radical cation, and neutral pyrazine.

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

Physics-Informed Gaussian Process Inference of Liquid Structure from Scattering Data

We present a nonparametric Bayesian framework to infer radial distribution functions from experimental scattering measurements with uncertainty quantification using nonstationary Gaussian processes. The Gaussian process prior mean and kernel functions are designed to mitigate well-known numerical challenges with the Fourier transform, including discrete measurement binning and detector windowing, while encoding fundamental yet minimal physical knowledge of the liquid structure. We demonstrate uncertainty propagation of the Gaussian process posterior to unmeasured quantities of interest. Experimental radial distribution functions of liquid argon and water with uncertainty quantification are provided as both a proof of principle for the method and a benchmark for molecular models.

Chemical structure↗
DOE OSTI2021

Efficient Free Triplet Generation Follows Singlet Fission in Diketopyrrolopyrrole Polymorphs with Goldilocks Coupling

Microcrystal electron diffraction, grazing incidence wide-angle scattering, and UV–vis spectroscopy were used to determine the unit-cell structure and the relative composition of dimethylated diketopyrrolopyrrole H- and J-polymorphs within thin films subjected to vapor solvent annealing (VSA) for different times. The electronic structure and excited-state deactivation pathways of the different polymorphs were examined by transient absorption spectroscopy, conductive probe atomic force microscopy, and molecular modeling. We find that VSA initially converts amorphous films into mixtures of H- and J-polymorphs and promotes further conversion from H to J with longer VSA times. Here, though both polymorphs exhibit efficient SF to form coupled triplets, free triplet yields are higher in J-polymorph films compared to mixed films because coupling in J-aggregates is lower and, in turn, more favorable for triplet decoupling.

36 MATERIALS SCIENCE↗
DOE OSTI2024

ACS Spotlight: Bipolar Membranes for Electrochemical Energy Conversion, Chemical Manufacturing, and Separations

Sustainable energy conversion, chemical manufacturing, and separations are central to addressing the world’s energy and environmental challenges. Electrochemical platforms stand as a cornerstone in addressing these challenges because they are low exergy and can be powered on renewable electrons. In electrochemical systems, bipolar membranes (BPMs) are emerging as a unique class of ion exchange membranes poised to revolutionize various electrochemical processes via pH control of anode and cathode chambers and in situ pH adjustment. In this Spotlight Review, we provide a comprehensive review of electrochemical platforms utilizing BPMs for energy conversion (water electrolyzers for hydrogen production, fuel cells, and flow batteries), chemical manufacturing (electrolyzers that convert carbon dioxide into value-added chemicals and nitrate into ammonia), and separations. The motivation for using BPMs, as well as their performance and durability, in electrochemical platforms are disseminated. We also discuss current challenges that impede BPM electrochemical systems from competing with state-of-the-art electrochemical systems using monopolar ion-exchange membranes (e.g., anion/hydroxide exchange membranes and cation/proton exchange membranes). Here, the review also covers molecular modeling and continuum modeling efforts to understand the basic mechanisms that govern BPM performance.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2020

Fluorescence Enhancement in the Solid State by Isolating Perylene Fluorophores in Metal–Organic Frameworks

Polycyclic aromatic hydrocarbons such as perylene, pyrene, and their derivatives are highly emissive fluorophores in solution. Furthermore, the practical applications of these materials in the field of molecular electronic and light emitting devices are often hindered by self-quenching effects due to the formation of non-fluorescent aggregates in concentrated solutions or in the solid state. Herein, we demonstrate that aggregation caused quenching of perylenes can be minimalized by molecular incorporation into metalorganic frameworks (MOFs). This study utilized a stable Zr 6 cluster-based MOF, UiO-67, as a matrix. Linear linkers containing the photo-responsive moieties were designed and incorporated into the parent UiO-67 scaffold through the partially replacement of the non-fluorescent linkers of a similar length, forming mixed-linker MOFs. Here, the average distance between perylene moieties was tuned by changing the linker ratios, thus controlling the fluorescence intensity, emission wavelength, and quantum yield. Molecular modeling was further adopted to correlate the number of isolated perylene linkers within the framework to the ratio between the two linkers, therefore rationalizing the change in the observed fluorescent properties. Taking advantage of the tunable fluorescence, inherent porosity, and high chemical stability of this MOF platform, it was applied as a fluorescent sensor for oxygen detection in the gas phase, a model reaction, showing fast response and good recyclability.

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

H 2 O and CO 2 Sorption in Ion-Exchange Sorbents: Distinct Interactions in Amine Versus Quaternary Ammonium Materials

This article examines how water (H₂O) and carbon dioxide (CO₂) interact with two classes of ion-exchange sorbents — a primary amine sorbent and a quaternary ammonium (QA⁺) sorbent — using calorimetry, thermal gravimetric analysis, gas analysis, and molecular modeling. Here, the QA⁺ sorbent exhibits stronger binding to both H₂O and CO₂ but also shows thermal stability limitations. Mixed-gas experiments reveal that humidity strongly influences CO₂ uptake and that moisture-driven sorbent regeneration enables cyclic moisture swing CO₂ capture, with implications for low-energy CO₂ separation from dilute gas streams.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Fast Advective Water Flow through Nanochannels in Clay Interlayers: Implications for Moisture Transport in Soils and Unconventional Oil/Gas Production

Water flow in nanometer or sub-nanometer hydrophilic channels bears special importance in diverse fields of science and engineering. However, the nature of such water flow remains elusive. In this work, we report our molecular-modeling results on water flow in a sub-nanometer clay interlayer between two montmorillonite layers. We show that a fast advective flow can be induced by evaporation at one end of the interlayer channel, that is, a large suction pressure created by evaporation (~818 MPa) is able to drive the fast water flow through the channel (~0.88 m/s for a 46 Å-long channel). Scaled up for the pressure gradient to a 2 μm particle, the velocity of water is estimated to be about 95 μm/s, indicating that water can quickly flow through a μm-sized clay particle within seconds. The prediction seems to be confirmed by our thermogravimetric analysis of bentonite hydration and dehydration processes, which indicates that water transport at the early stage of the dehydration is a fast advective process, followed by a slow diffusion process. The possible occurrence of a fast advective water flow in clay interlayers prompts us to reassess water transport in a broad set of natural and engineered systems such as clay swelling/shrinking, moisture transport in soils, water uptake by plants, water imbibition/release in unconventional hydrocarbon reservoirs, and cap rock integrity of supercritical CO 2 storage.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

Amino Acid Sequence Controls Enhanced Electron Transport in Heme-Binding Peptide Monolayers

Metal-binding proteins have the exceptional ability to facilitate long-range electron transport in nature. Despite recent progress, the sequence-structure–function relationships governing electron transport in heme-binding peptides and protein assemblies are not yet fully understood. In this work, the electronic properties of a series of heme-binding peptides inspired by cytochrome bc1 are studied using a combination of molecular electronics experiments, molecular modeling, and simulation. Self-assembled monolayers (SAMs) are prepared using sequence-defined heme-binding peptides capable of forming helical secondary structures. Following monolayer formation, the structural properties and chemical composition of assembled peptides are determined using atomic force microscopy and X-ray photoelectron spectroscopy, and the electronic properties (current density–voltage response) are characterized using a soft contact liquid metal electrode method based on eutectic gallium–indium alloys (EGaIn). Our results show a substantial 1000-fold increase in current density across SAM junctions upon addition of heme compared to identical peptide sequences in the absence of heme, while maintaining a constant junction thickness. These findings show that amino acid composition and sequence directly control enhancements in electron transport in heme-binding peptides. Overall, this study demonstrates the potential of using sequence-defined synthetic peptides inspired by nature as functional bioelectronic materials.

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

Absolute Templating of M(111) Cluster Surrogates by Galvanic Exchange

The precise preparation of monodisperse nanomaterials is among the most fundamental tasks in inorganic synthesis and materials science. Achieving this goal by galvanic exchange is hardly predictable, and often results in major structural changes and polydisperse mixtures. Here, taking advantage of the enhanced stability imparted by ambiphilic carbenes, we report and rationalize the absolute templating — the complete exchange of metals in a template — of group 11 clusters across the entire coinage metal family by means of galvanic exchange. We further delineate that these species provide a molecular model for better understanding the reduction of CO 2 at M(111) coinage metal surfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗