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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 OSTI2026

Elucidating molecular level interfacial interactions between a de novo protein and nucleated calcite with solid-state NMR

Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic–inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. Here, to understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31–calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ∼2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31–calcite interactions. While this work provides the first experimental confirmation that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31–calcite interface has advanced our fundamental understanding of the atomic interactions at the organic–inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.

Close, Emily G. S. [Pacific Northwest National Lab↗
DOE OSTI2025

DataSet for Elucidating molecular level interfacial interactions between a de novo protein and nucleated calcite with solid-state NMR

Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic-inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. To understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31-calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ~2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31-calcite interactions. These studies provide the first experimental evidence to confirm that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template. However, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31-calcite interface has advanced our fundamental understanding of the atomic interactions at the organic-inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.

Saccuzzo Close, Emily Grace [Pacific Northwest Nat↗
DOE OSTI2020

Measurement of atom resolvability in cryo-EM maps with Q-scores

Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Here, assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Tiny Sc Allows the Chains to Rattle: Impact of Lu and Y Doping on the Charge-Density Wave in ScV 6 Sn 6

The kagome metals display an intriguing variety of electronic and magnetic phases arising from the connectivity of atoms on a kagome lattice. A growing number of these materials with vanadium–kagome nets host charge–density waves (CDWs) at low temperatures, including ScV 6 Sn 6 , CsV 3 Sb 5 , and V 3 Sb 2 . Curiously, only the Sc version of the RV 6 Sn 6 materials with a HfFe 6 Ge 6 -type structure hosts a CDW (R = Gd–Lu, Y, Sc). In this study, we investigate the role of rare earth size in CDW formation in the RV 6 Sn 6 compounds. Magnetization measurements on our single crystals of (Sc,Lu)V 6 Sn 6 and (Sc,Y)V 6 Sn 6 establish that the CDW is suppressed by substituting Sc by larger Lu or Y. Single-crystal X-ray diffraction reveals that compressible Sn–Sn bonds accommodate the larger rare earth atoms within loosely packed R–Sn–Sn chains without significantly expanding the lattice. We propose that Sc provides extra room in these chains crucial to CDW formation in ScV 6 Sn 6 . Our rattling chain model explains why both physical pressure and substitution by larger rare earth atoms hinder CDW formation despite opposite impacts on lattice size. Here, we emphasize the cooperative effect of pressure and rare earth size by demonstrating that pressure further suppresses the CDW in a Lu-doped ScV 6 Sn 6 crystal. Our model not only addresses why a CDW only forms in the RV 6 Sn 6 materials with tiny Sc but also advances our understanding of why unusual CDWs form in the kagome metals.

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

Ultra-large-scale ab initio quantum chemical computation of bio-molecular systems: The case of spike protein of SARS-CoV-2 virus

The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intramolecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Lower bounds on entanglement entropy without twin copy

We discuss the possibility of estimating experimentally the von Neumann entanglement entropy S A v N of a symmetric bipartite quantum system A B by using the basic measurement counts (bitstrings) for a single copy of a prepared state. Using exact diagonalization and analog simulations performed with the publicly available QuEra facilities for chains and ladders of Rydberg atoms, we calculate the Shannon entropy S A B X associated with the bitstrings of adiabatically prepared ground states and the reduced entropies S A X and S B X obtained from the marginal probabilities in A and B . We then calculate the classical mutual information I A B X = S A X + S B X − S A B X , which is a lower bound on S A v N . We show that for a broad range of lattice spacing and detuning, I A B X is typically 20% below S A v N in regions where S A v N is large and a less close bound in regions where S A v N is low. We argue that this use of the easily available bitstrings provides a robust and efficient way to explore empirically the phase diagram of qubit-based quantum simulators and identify critical regions. Published by the American Physical Society 2025

Meurice, Yannick (ORCID:0000000209959694)↗
DOE OSTI2020

Coexistence of Soft Modes and Dynamic Ti Disorder in Cubic BaTiO 3 Studied by Inelastic Neutron Scattering

The phonon dispersion relations in cubic BaTiO 3 have been measured along the [100], [110], and [111] directions at T = 453 K using inelastic neutron scattering. The isotropic transverse acoustic (TA) branches indicate that the interatomic force constant between Ba and O atoms in BaTiO 3 is large compared with that between Pb and O atoms in PbTiO 3 . The transverse optical (TO) branches along the [100] and [111] directions soften toward the Brillouin zone center. The TO branch along the [110] direction with [001] polarization is relatively low and flat, indicating the weak interatomic force constant between Ti and O atoms along the Ti–O chain. The intensity of inelastic diffuse scattering along the [100] and [110] directions increases with decreasing temperature down to 453 K. In conclusion, the present results suggest that the soft modes coexist with the dynamic Ti disorder in the Ti–O chain near the phase transition in the cubic phase.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS1978

Polymers with complexing properties. Simple poly(amino acids)

The free amino (0.3 equiv/residue) and carboxyl (0.5 equiv/residue) groups of thermal polylysine increased dramatically on treatment with distilled water. The total hydrolysis of such a polymer was abnormal in that only about 50% of the expected amino acids were recovered. Poly (lysine-co-alanine-co-glycine) under usual conditions hydrolyzed completely in 8 hours; whereas, when it was pretreated with diazomethane, a normal period of 24 hours was required to give (nearly) the same amounts of each free amino acid as compared with those obtained from the untreated polymer. The amino groups of the basic thermal poly(amino acids) were sterically hindered. The existence of nitrogen atoms linking two or three chains and reactive groups (anhydride, imine) were proposed.

Roque, J. M.↗
NASA NTRS1982

Probing the presently tenuous link between comets and the origin of life

The possibilities of using millimeter-wave technology to probe the subsurface processes of comets to investigate links between cometary materials and the origins of life are explored. It is noted that current theories hold that the necessities for life to begin comprise a fairly uniform temperature, the presence of a solvent to give materials mobility, and the presence of atoms which can form long chains of molecules. Consideration is given to two cometary nuclei models: a core with an equal amount of liquid water and lunar material, and a nucleus with equal amounts of frozen water ice and lunar material. Solutions to the radiative transfer equation for the two models are presented to characterize identifiable emissions using radiometric spectrometer instrumentation on a spacecraft. Particular species such as OH, CN, HCN, and glycine are expected to be detectable if present.

Hobbs, R. W.↗
NASA NTRS1999

What is the Best Alternative to Diagonalization of the Hamiltonian in Large Scale Semiempirical Calculations?

Recently, several linear scaling approaches have been introduced which replace the time dominating diagonalization step in semiempirical methods, enabling practical calculations to be performed, on very large molecules. This paper compares the accuracy and performance of pseudodiagonalization (PD), conjugate gradient density matrix search (CG-DMS), the Chebyshev polynomial expansion method (CEM), and purification of the density matrix (PDM) as linear scaling substitutions for diagonalization. The scaling, speed, and reliability of these methods are compared for AMI single point energy calculations on polyglycine chains (up to 20,000 atoms), water clusters (up to 12,300 atoms), and nucleic acids (up to 6300 atoms).

Daniels, Andrew D.↗
DOE OSTI2025

Side-Chain and Ring-Size Effects on Permeability in Artificial Water Channels

Artificial water channels (AWCs) have emerged as a promising framework for stable water permeation, with water transport rates comparable to aquaporins (3.4–40.3 × 10 8 H 2 O/channel/s). In this study, we probe the influence of ring-size and side-chain length on the water permeability observed within a class of AWCs termed ligand-appended pillar[n]arenes (LAPs) that have an adjustable ring-size (m) and side-chain length (n). Through all-atom molecular dynamics simulations, we calculate the permeability of these channels using the collective diffusion model and find their permeabilities. We characterize the mechanistic influence of pillar[n]arene ring-size and side-chain length on the channel water permeability by analyzing the characteristics of the internal permeating water-wire and the surrounding channel structure. We observe that water permeability decreases as a function of increasing ring-size due to increases in hydrophilic contacts between the permeating water-wire and the oxygen groups on the channel wall. Further, we observe an increase in water permeability as a function of side-chain length due to increased partitioning of the channel terminal groups into the hydrophilic blocks of the surrounding bilayer. For the LAP6 channel, with increase in side-chain length, the distance between terminal groups increases and leads to an increase in pore size, thereby enhancing water permeability. In the case of LAP5, as side-chain length increases, the channel displays a compensatory effect between tilt and bend angle due to the flexible side-chains. Such flexibility leads to higher terminal group partitioning in the hydrophilic blocks of the bilayer and extends the permeating water-wire. Furthermore, this increase in water-wire length and hydrophilic block access overcomes the nonmonotonic pore size trend in pillar[5]arene channels.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics

Lipid bilayers form the main matrix of functional cell membranes, and their dynamics underlie a host of physical and biological processes. Here we show that elastic membrane properties and collective molecular dynamics (MD) are related by the mean-square amplitudes (order parameters) and relaxation rates (correlation times) of lipid acyl chain motions. We performed all-atom MD simulations of liquid-crystalline bilayers that allow direct comparison with carbon-hydrogen (CH) bond relaxations measured with NMR spectroscopy. Previous computational and theoretical approaches have assumed isotropic relaxation, which yields inaccurate description of lipid chain dynamics and incorrect data interpretation. Instead, the new framework includes a fixed bilayer normal (director axis) and restricted anisotropic motion of the CH bonds in accord with their segmental order parameters, enabling robust validation of lipid force fields. Simulated spectral densities of thermally excited CH bond fluctuations exhibited well-defined spin-lattice (Zeeman) relaxations analogous to those in NMR measurements. Their frequency signature could be fit to a simple power-law function, indicative of nematic-like collective dynamics. Moreover, calculated relaxation rates scaled as the squared order parameters yielding an apparent K C modulus for bilayer bending. Our results show a strong correlation with K C values obtained from solid-state NMR studies of bilayers without and with cholesterol as validated by neutron spin-echo measurements of membrane elasticity. The simulations uncover a critical role of interleaflet coupling in membrane mechanics and thus provide important insights into molecular sites of emerging elastic properties within lipid bilayers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cooperativity in the Aldol Condensation Using Bifunctional Mesoporous Silica–Poly(styrene) MCM-41 Organic/Inorganic Hybrid Catalysts

This work explores the efficacy of silica/organic hybrid catalysts, where the organic component is built from linear aminopolymers appended to the silica support within the support mesopores. Specifically, the role of molecular weight and polymer chain composition in amine-bearing atom transfer radical polymerization-synthesized poly(styrene-co-2-(4-vinylbenzyl)isoindoline-1,3-dione) copolymers is probed in the aldol condensation of 4-nitrobenzaldehyde and acetone. Controlled polymerization produces protected amine-containing poly(styrene) chains of controlled molecular weight and dispersity, and a grafting-to thiol–ene coupling approach followed by a phthalimide deprotection step are used to covalently tether and activate the polymer hybrid catalysts prior to the catalytic reactions. Site-normalized batch kinetics are used to assess the role of polymer molecular weight and chain composition in the cooperative catalysis. Lower-molecular-weight copolymers are demonstrated to be more active than catalysts built from only molecular organic components or from higher-molecular-weight chains. Molecular dynamics simulations are used to probe the role of polymer flexibility and morphology, whereby it is determined that higher-molecular-weight hybrid structures result in congested pores that inhibit active site cooperativity and the diffusivity of reagents, thus resulting in lower rates during the reaction.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Reactions of the ˙NO 3 radical with nuclear extraction ligands in alkane solution

Here, the reactivity of the nitrate radical (NO 3 ˙) with organophosphorus and amidic actinide and lanthanide complexing agents of interest to nuclear solvent extraction applications was measured, resulting in the first-ever reported bimolecular rate constants for this radicals’ reactions in dodecane solution. The order of reactivity for neutral organophosphorus compounds showed faster rate constants with increasing electron density on the phosphoryl phosphorus atom, indicating an increasing facility for electron abstraction reactions occurring in addition to H-atom abstraction from the ligand alkane chains. The only acidic organophosphorus compound investigated, HEH[EHP], showed low reactivity with the NO 3 ˙ radical, attributed to its dimerization in this non-polar solvent. Amide ligand reaction rates were faster than for organophosphorus molecules, suggesting more facile H-atom abstraction from carbonyl activated methylene and amyl groups. While all rate constants were slower than the diffusion-limited rate they were still rapid enough to result in significant oxidation of solvent extraction ligands in dodecane solution.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

Structure, Dynamics, and Hydrogen Transport in Amorphous Polymers: An Analysis of the Interplay between Free Volume Element Distribution and Local Segmental Dynamics from Molecular Dynamics Simulations

Polymers are attractive membrane materials owing to their mechanical robustness and relatively inexpensive fabrication. An important indicator of membrane performance are free volume elements (FVE): microporous void spaces created by the inefficient packing of bulky groups along the polymer chain. FVEs tend to degrade over time, as polymer chains reorganize irreversibly. While it is widely accepted that polymer flexibility has an impact on membrane transport properties, the molecular nature of this impact is still not well understood. By the establishment of a correlation between local chain dynamics and the distribution of free volume elements (FVEs), penetrant transport can be regulated more efficiently in amorphous polymer membranes. In this work, we implement all-atom molecular dynamics (MD) simulations to explore the relationship between chain dynamics and free volume in three polymers with different levels of backbone flexibility: polymethylpentene (PMP), polystyrene (PS), and HAB-6FDA thermally rearranged polymer (TRP). We construct these polymers at different temperatures and examine how temperature impacts the FVE distribution and segmental mobility. Our analysis shows that chain segments near FVEs have higher mobility compared with the atoms in the bulk; the extent of this difference increases with chain flexibility. Increasing the chain flexibility by increasing the temperature results in a broader FVE distribution. Rigid polymers such as TRP show the most robust FVE distribution and are not significantly affected by the temperature change. To capture penetrant diffusion through the polymer matrix, hydrogen is inserted and the diffusion is measured at different temperatures; hydrogen mobility is influenced by the FVE structure and overall mobility of polymer chains. Lastly, at low temperatures, hydrogen mobility is influenced by void distribution, while at high temperatures, polymer dynamics dictate hydrogen transport.

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

Spin and charge density waves in quasi-one-dimensional KMn 6 Bi 5

The recent observation that pressure could suppress antiferromagnetic (AFM) order in quasi-one-dimensional AMn 6 Bi 5 Mn-cluster chain materials (A=Na, K, Rb, and Cs) and lead to a superconducting dome offers an alternative Mn-based class of materials with which to study unconventional superconductivity. Using neutron diffraction, we elucidate the exact nature of the previously unknown AFM ground state of KMn 6 Bi 5 and report finding transverse incommensurate spin density waves (SDWs) for the Mn atoms with a propagating direction along the chains. The SDWs have distinct refined amplitudes of ~2.46μ B for the Mn atoms in the pentagons and ~0.29μ B with a large standard deviation for Mn atoms at the center between the pentagons. AFM coupling dominates both the nearest-neighbor Mn-Mn interactions within the pentagon and next-nearest-neighbor Mn-Mn interactions out of the pentagon (along the propagating wave). The SDWs exhibit both local and itinerant characteristics potentially due to cooperative interactions between local magnetic exchange and conduction electrons. Single crystal x-ray diffraction below the AFM transition revealed satellite peaks originating from charge density waves along the chain direction with a q vector twice as large as that of the SDW, pointing to a strong real space coupling between them. Additionally, we report a significant magnetoelastic effect during the AFM transition, especially along the chain direction, observed in temperature-dependent x-ray powder diffraction. Our work not only reveals fascinating intertwined spin, charge, and lattice orders in one-dimensional KMn 6 Bi 5 , but also provides an essential piece of information on its magnetic structure to understand the mechanism of superconductivity in this Mn-based family.

1-dimensional systems↗
DOE OSTI2023

Atomic-scale cryogenic electron microscopy imaging of self-assembled peptoid nanostructures

Amphiphilic polypeptoids with defined sequences, versatile in forming various nanostructures, are ideal for mimicking biomacromolecular structures. The predictive design of nanostructures depends on our understanding of the relationship between molecular structure and the locations of atoms in the nanostructure. Factors of importance include chain conformation, crystal motifs, and the arrangement of the molecules within the nanostructure. Here, this review introduces the cryogenic transmission electron microscopy (cryo-TEM) method, sorting and averaging unit cells in nanosheets for resolution enhancement and identifying structural heterogeneity. The resulting atomic-scale images reveal the presence of two types of crystal motifs. The impact of processing conditions, capping group chemistry, and side chain chemistry on structural heterogeneity and crystal motifs can be quantified. The 3D reconstruction of nanosheets, wherein atomic-scale corrugations were revealed, is introduced in this review. New developments in cryo-TEM, such as phase retrieval reconstruction, hold great promise for atomic-scale imaging of soft nanostructures.

36 MATERIALS SCIENCE↗