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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Quantification of Brønsted Acid Sites in Zeolites by Water Desorption Thermogravimetry

The many studies that have been conducted on water adsorption on zeolites were carried out in “adsorption” mode, from adsorption isotherms or single-point measurements, with the samples being first degassed at high temperature, and then exposed to water vapor at variable partial pressure. Here, we report Thermogravimetric Analysis (TGA) studies of HZSM-5 saturated with water at room temperature, thus studying water adsorption in “desorption” mode. In this work, TGA was used to ascertain the amount of water remaining as a function of the pretreatment temperature, and to identify the temperature at which one water molecule per framework Al atom persists. Solid-state 1H NMR spectroscopy, combined with molecular modeling, provided evidence for water molecules hydrogen bonded to Brønsted acid sites and formation of oxonium species for distinct water per framework Al atom. TGA is shown to be a simple and expeditious technique to measure the number of Brønsted acid sites in aluminosilicate zeolites, with advantages over the traditional methods of IR or TPD of dangerous adsorbed ammonia or pyridine. TGA of adsorbed water also provides information on the water clusters formed at the acid sites of HZSM-5, which are proportional to the number of acid sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Insight into the autoproteolysis mechanism of the RsgI9 anti‐σ factor from Clostridium thermocellum

Abstract Clostridium thermocellum is a potential microbial platform to convert abundant plant biomass to biofuels and other renewable chemicals. It efficiently degrades lignocellulosic biomass using a surface displayed cellulosome, a megadalton sized multienzyme containing complex. The enzymatic composition and architecture of the cellulosome is controlled by several transmembrane biomass‐sensing RsgI‐type anti‐σ factors. Recent studies suggest that these factors transduce signals from the cell surface via a conserved RsgI extracellular (CRE) domain (also called a periplasmic domain) that undergoes autoproteolysis through an incompletely understood mechanism. Here we report the structure of the autoproteolyzed CRE domain from the C. thermocellum RsgI9 anti‐σ factor, revealing that the cleaved fragments forming this domain associate to form a stable α/β/α sandwich fold. Based on AlphaFold2 modeling, molecular dynamics simulations, and tandem mass spectrometry, we propose that a conserved Asn‐Pro bond in RsgI9 autoproteolyzes via a succinimide intermediate whose formation is promoted by a conserved hydrogen bond network holding the scissile peptide bond in a strained conformation. As other RsgI anti‐σ factors share sequence homology to RsgI9, they likely autoproteolyze through a similar mechanism.

Takayesu, Allen↗
DOE OSTI2024

Phosphorus recycling by mineral-catalyzed ribonucleotide cleavage on iron and manganese oxides

Abstract Phosphorus is an essential element influencing both food security via plant fertilization, and water pollution through excessive phosphorus use, yet the phosphorus cycle in ecosystems is poorly known. In particular, beyond adsorption, the role of iron and manganese oxides in catalyzing the abiotic dephosphorylation of biomolecules is debated. Here, we studied the reactions of ribonucleotides, containing different phosphate bonding, with goethite, hematite, and birnessite. We employed both high-resolution mass spectrometry of solution species and molecular modeling simulations of ribonucleotide-mineral complexes. Results disclose an up to fivefold preferential hydrolytic cleavage of a phosphoanhydride bond over a phosphoester bond, indicating that mineral-catalyzed reactions reflect the hierarchy reported for the activity of phosphatase enzymes. The fourfold higher catalytic reactivity of goethite and birnessite versus hematite is explained by mineral-specific binding rather than surface area differences. Corresponding simulated adsorbate conformations at the water–mineral interfaces are proposed. Overall, our findings provide new insights on the catalytic recycling of organic phosphorus species by mineral oxides.

58 GEOSCIENCES↗
DOE OSTI2021

New insights into creep characteristics of calcium silicate hydrates at molecular level

The fundamental mechanisms under concrete creep are far from being fully understood, especially at the molecular level. Hereby, a calcium-silicate-hydrate (C-S-H) molecular model is developed to explain, for the first time, the creep characteristics at various stress states, temperature levels and water contents, which are not accessible experimentally. Rather tensile and compressive loadings, C-S-H only creeps under shear loadings originating from the sliding of the calcium silicate layers over each other as the interlayer component (water and ions) acts as a lubricator. A heterogeneous creep characteristic is observed. Elevated temperature reduces the interlayer lubricator viscosity and weakens the interfacial adhesion between the layers and the interlayer lubricator, which accelerates C-S-H creep. The removal of interlayer water enhances the creep resistance, resulting from the reduced interlayer space and enhanced interfacial adhesion. The atomic-level mechanisms explain the inter-CSH-particle behaviours at the microscale, which bridges the gap between atomistic simulation and microcosmic phenomenon.

36 MATERIALS SCIENCE↗
DOE OSTI2021

PIM-induced phosphorylation of Notch3 promotes breast cancer tumorigenicity in a CSL-independent fashion

Dysregulation of the developmentally important Notch signaling pathway is implicated in several types of cancer, including breast cancer. However, the specific roles and regulation of the four different Notch receptors have remained elusive. We have previously reported that the oncogenic PIM kinases phosphorylate Notch1 and Notch3. Phosphorylation of Notch1 within the second nuclear localization sequence of its intracellular domain (ICD) enhances its transcriptional activity and tumorigenicity. In this study, we analyzed Notch3 phosphorylation and its functional impact. Unexpectedly, we observed that the PIM target sites are not conserved between Notch1 and Notch3. Notch3 ICD (N3ICD) is phosphorylated within a domain, which is essential for formation of a transcriptionally active complex with the DNA-binding protein CSL. Through molecular modeling, X-ray crystallography, and isothermal titration calorimetry, we demonstrate that phosphorylation of N3ICD sterically hinders its interaction with CSL and thereby inhibits its CSL-dependent transcriptional activity. Surprisingly however, phosphorylated N3ICD still maintains tumorigenic potential in breast cancer cells under estrogenic conditions, which support PIM expression. Taken together, our data indicate that PIM kinases modulate the signaling output of different Notch paralogs by targeting distinct protein domains and thereby promote breast cancer tumorigenesis via both CSL-dependent and CSL-independent mechanisms.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Biophysical analysis of the plant-specific GIPC sphingolipids reveals multiple modes of membrane regulation

The plant plasma membrane (PM) is an essential barrier between the cell and the external environment, controlling signal perception and transmission. It consists of an asymmetrical lipid bilayer made up of three different lipid classes: sphingolipids, sterols, and phospholipids. The glycosyl inositol phosphoryl ceramides (GIPCs), representing up to 40% of total sphingolipids, are assumed to be almost exclusively in the outer leaflet of the PM. However, their biological role and properties are poorly defined. In this study, we investigated the role of GIPCs in membrane organization. Because GIPCs are not commercially available, we developed a protocol to extract and isolate GIPC-enriched fractions from eudicots (cauliflower and tobacco) and monocots (leek and rice). Lipidomic analysis confirmed the presence of trihydroxylated long chain bases and 2-hydroxylated very long-chain fatty acids up to 26 carbon atoms. The glycan head groups of the GIPCs from monocots and dicots were analyzed by gas chromatograph-mass spectrometry, revealing different sugar moieties. Multiple biophysics tools, namely Langmuir monolayer, ζ-Potential, light scattering, neutron reflectivity, solid state 2H-NMR, and molecular modeling, were used to investigate the physical properties of the GIPCs, as well as their interaction with free and conjugated phytosterols. We showed that GIPCs increase the thickness and electronegativity of model membranes, interact differentially with the different phytosterols species, and regulate the gel-to-fluid phase transition during temperature variations. These results unveil the multiple roles played by GIPCs in the plant PM.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA

Metazoan microRNAs require specificmaturation steps initiated by Microprocessor, comprising Drosha and DGCR8. Lack of structural information for the assembled complex has hindered an understanding of how Microprocessor recognizes primary microRNA transcripts (pri-miRNAs). In this paper we present a cryoelectron microscopy structure of human Microprocessor with a pri-miRNA docked in the active site, poised for cleavage. The basal junction is recognized by a four-way intramolecular junction in Drosha, triggered by the Belt and Wedge regions that clamp over the ssRNA. The belt is important for efficiency and accuracy of pri-miRNA processing. TwodsRBDs form a molecular ruler tomeasure the stem length between the twodsRNA-ssRNAjunctions. The specific organization of thedsRBDs near the apical junction is independent of Drosha core domains, as observed in a second structure in the partially docked state. Collectively, we derive a molecular model to explain how Microprocessor recognizes a pri-miRNA and accurately identifies the cleavage site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Selectivity of enzymes involved in the formation of opposite enantiomeric series of p -menthane monoterpenoids in peppermint and Japanese catnip

Peppermint (Mentha x piperita L.) and Japanese catnip (Schizonepeta tenuifolia (Benth.) Briq.) accumulate p-menthane monoterpenoids with identical functionalization patterns but opposite stereochemistry. In the present study, we investigate the enantioselectivity of multiple enzymes involved in monoterpenoid biosynthesis in these species. Based on kinetic assays, mint limonene synthase, limonene 3-hydroxylase, isopiperitenol dehydrogenase, isopiperitenone reductase, and menthone reductase exhibited significant enantioselectivity toward intermediates of the pathway that proceeds through (-)-4S-limonene. Limonene synthase, isopiperitenol dehydrogenase and isopiperitenone reductase of Japanese catnip preferred intermediates of the pathway that involves (+)-4R-limonene, whereas limonene 3-hydroxylase was not enantioselective, and the activities of pulegone reductase and menthone reductase were too low to acquire meaningful kinetic data. Molecular modeling studies with docked ligands generally supported the experimental data obtained with peppermint enzymes, indicating that the preferred enantiomer was aligned well with the requisite cofactor and amino acid residues implicated in catalysis. A striking example for enantioselectivity was peppermint (-)-menthone reductase, which binds (-)-menthone with exquisite affinity but was predicted to bind (+)-menthone in a non-productive orientation that positions its carbonyl functional group at considerable distance to the NADPH cofactor. Here, the work presented here lays the groundwork for structure-function studies aimed at unraveling how enantioselectivity evolved in closely related species of the Lamiaceae and beyond.

59 BASIC BIOLOGICAL SCIENCES↗
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↗