Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Atomic & molecular structure”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
NASA NTRS2017

A Spaceflight Experiment to Determine the Effect of Chamfered Sample Holders on Atomic Oxygen Erosion

The exteriors of low Earth orbit (LEO) spacecraft are subjected to many environmental threats that can cause the surface materials to degrade. One of these threats is atomic oxygen (AO), which is formed by photo dissociation of molecular oxygen by energetic UV radiation. Atomic oxygen exposure can result in oxidative erosion of polymers leading to structural or thermal failure of spacecraft components. The amount of AO erosion expected during a mission can be calculated by knowing the AO erosion yield (Ey, volume loss per incident atom) of the material and the AO fluence expected for the mission. The Ey can be determined through dehydrated mass loss measurements of test samples if one knows the AO fluence, density, and exposure area. Such measurements have been made as part of flight experiments, including the Materials International Space Station Experiment 2 (MISSE 2) Polymers Experiment. The MISSE 2 Polymers Experiment sample holders had chamfered circular apertures that controlled the exposure area, but also allowed some additional AO to scatter from the chamfered edges onto the samples thus causing some samples to erode thru and peel at their perimeter due to this scattering effect. By modeling the scattered AO flux one can predict the actual total AO fluence, and hence more accurate sample Ey. Sample holders with different chamfered-perimeter to exposed-area ratios have been designed for future spaceflight experiments that allow a more accurate determination of the Ey for large area polymers, representative of their use on spacecraft surfaces.

Earth Orbital Environments↗
NASA NTRS1992

The effects of molecular structure on the electrical conductivity of polymers

The role of Quantum Theoretical Methods is both predictive and supportive of experimental results in Chemistry. Present day methods are able to calculate vibrational spectra and stereochemical interactions for molecules of moderate size (up to 20 atoms). As for the predictive side, the electronic structure of molecules and polymers can be calculated in order to narrow down the field of many potential candidates, which would have the novel properties looked for. The following has been accomplished at the Rutgers Camden Chemistry Department as results of calculations on molecular and polymeric systems of interest to the Polymers Branch of the NASA Lewis Research Center, under Grant NAG3-956.

Burke, Luke A.↗
DOE OSTI2023

Dynamics of plasma atomic layer etching: Molecular dynamics simulations and optical emission spectroscopy

Atomic layer etching is intrinsically dynamic as it involves sequential and repeated exposures of a surface to be etched with different species at different energies. The composition and structure of the near surface region change in both time and depth. Full understanding of this process requires resolving both temporal and spatial variations. In this work, we consider silicon (Si) atomic layer etching (ALE) by alternating exposure to chlorine gas (Cl 2 ) and argon ions (Ar + ). Molecular dynamics (MD) simulations are compared to experimental measurements with the aim of better understanding the dynamics of ALE and to test the simulation procedure. The simulations help to more fully interpret the experimental measurements. Further, optical emission measured just above the surface being etched can be related to etch products and can, therefore, be directly compared to simulation predictions. The simulations capture the measured initial product distribution leaving the surface and match the measured etch per cycle reasonably well. While simulations demonstrate the importance of ion-induced surface damage and mixing into a layer below the surface, the depth of which depends mainly on ion energy, the experiments suggest there is more Cl mixed into the layer than the MD procedure predicts.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

Strong-field Driven Sub-cycle Band Structure Modulation and Dephasing Control

In this work, we present measurements of ultrafast electric-field observables in magnesium oxide using a non-resonant nonlinear optical interaction. Using field observables, we show that strong laser fields modulate the band structure on sub-cycle timescales, thereby altering the material’s nonlinear optical response. We perform time-dependent perturbation theory calculations using a field-dependent dispersion relation and semiconductor Bloch equation calculations, both of which agree with experimental observations. Furthermore, we extract pulse decay times from the real-time signal electric field envelope and show sub-cycle control of dephasing times. Our work offers a new perspective on strong-field-driven electron dynamics in solids through electric-field observables. The demonstrated attosecond modulation of the nonlinear response could have important implications for quantum light generation and quantum spectroscopy using nonlinear optical processes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Structural origin of disorder-induced ion conduction in NaFePO 4 cathode materials

Diffusion in NaFePO 4 can be enhanced through amorphization. Based on computations using DFT and machine learning potentials, we ascribe this phenomenon to the formation of less constrained Na-ion environments upon disordering. Most modern battery technologies depend on solid-state crystalline cathode materials. However, some of these materials are constrained by the low ionic conductivity of their most stable phases. An example of this is maricite (NaFePO 4 ). Interestingly, experiments have shown that maricite can improve its rate capability through disordering (amorphization). However, experimental characterization of amorphous cathode materials remains a major challenge, hindering a clear understanding of the structural origin of the disorder-induced improvement in sodium-ion mobility. To address this, we here employ molecular dynamics simulations by first training a machine learning potential for NaFePO 4 based on the atomic cluster expansion approach and a batch active learning potential parameterization scheme. This potential is then applied to explore the structural and dynamical properties of NaFePO 4 glasses as cathode materials. Specifically, we investigate the effect of glass structure on sodium-ion diffusion, revealing the relative influences of short-range and medium-range order features. We find significant heterogeneity in sodium-ion diffusivity in the glass, with fast-conducting ions residing in less constrained atomic environments with fewer P and Fe neighbors. These more mobile ions are also surrounded by larger ring-type structures. Overall, the results and developed approach present promising avenues for developing high-performance glassy cathodes for next-generation batteries.

Christensen, Rasmus↗
DOE OSTI2021

Transformation of atomically dispersed platinum in SAPO-37 into platinum clusters: catalyst for ethylene hydrogenation

Atomically dispersed supported platinum catalysts were synthesized by the reaction of Pt(acac) 2 (acac = acetylacetonato) with the silicoaluminophosphate molecular sieve SAPO-37, with infrared spectra showing that the reaction involved SAPO OH groups. Extended X-ray absorption fine structure (EXAFS) spectra show that, after heating in air to 623 K, each platinum atom on average was bonded to approximately two oxygen atoms of the SAPO support, with no evidence of platinum clusters. X-ray absorption near edge spectra (XANES) indicate a platinum formal oxidation state of approximately +2. Here, these supported mononuclear species lacked catalytic activity for ethylene hydrogenation at 1 bar and room temperature, but activity arose during catalysis in a once-through flow reactor/X-ray absorption spectroscopy cell, as the XANES white line intensity decreased, indicating reduction of the platinum, and the EXAFS-determined Pt–Pt coordination number (CN) increased from essentially zero to 2.7 ± 0.5 after 2 h, indicating the formation of platinum clusters of only a few atoms each. The data indicate the almost instantaneous formation of the clusters and identify them as the catalytically active species. Subsequent exposure of the catalyst to ethylene as in situ EXAFS and XANES data were recorded led to a decrease in the Pt–Pt coordination number to 1.6 ± 0.3 and an increase in the white line intensity, indicating partial oxidative fragmentation of the clusters by ethylene. Platinum clusters in SAPO-37 formed in separate experiments by exposure to H 2 prior to catalysis were also catalytically active for ethylene hydrogenation. Here, the data thus show how to dial in the catalytic activity by forming platinum clusters by exposure of mononuclear platinum to H 2 and how to dial back the activity by oxidative fragmentation of the clusters by reaction with ethylene, all under mild conditions; the ethylene : H 2 ratio of the reactant gas determines the average platinum nuclearity and thus the catalytic activity.

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

Equation-of-motion internally contracted multireference unitary coupled-cluster theory

The accurate computation of excited states remains a challenge in electronic structure theory, especially for systems with a ground state that requires a multireference treatment. In this work, we introduce a novel equation-of-motion (EOM) extension of the internally contracted multireference unitary coupled-cluster framework (ic-MRUCC), termed EOM-ic-MRUCC. EOM-ic-MRUCC follows the transform-then-diagonalize approach, in analogy to its non-unitary counterpart. By employing a projective approach to optimize the ground state, the method retains additive separability and proper scaling with system size. We show that excitation energies are size-intensive if the EOM operator satisfies the “killer” and the projective conditions. Furthermore, we propose to represent changes in the reference state upon electron excitation via projected many-body operators that span the active orbitals and show that the EOM equations formulated in this way are invariant with respect to active orbital rotations. We test the EOM-ic-MRUCC method truncated to single and double excitations by computing the potential energy curves for several excited states of a BeH2 model system, the HF molecule, and water undergoing symmetric dissociation. Across these systems, our method delivers accurate excitation energies and potential energy curves within 5 mE h (∼0.14 eV) from full configuration interaction. Here, we find that truncating the Baker–Campbell–Hausdorff series to fourfold commutators contributes negligible errors (on the order of 10 −5 E h or less), offering a practical route to highly accurate excited-state calculations with reduced computational overhead.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

On the role of methyl groups in the molecular architectures of mesophase pitches

The role of methyl groups on the liquid–crystal structure of mesophase pitches was investigated by combining experimental characterizations and atomic-scale computational modeling, using three pitches synthesized from different precursors. Of the three pitches, C-9 alkyl benzene and naphthalene-based pitches have 13 and 7 methyl groups per average polyaromatic hydrocarbon, respectively. By contrast, mesophase produced from a coal-tar pitch has about one methyl group. The coal tar–based mesophase pitch is hydrogen deficient or more aromatic compared with C-9 alkyl benzene- and naphthalene-based pitches. Additionally, X-ray diffraction data showed that average coherent domain sizes of C-9 alkyl benzene (3.7 nm) and naphthalene-based (3.6 nm) pitches with more methyl groups are larger than that of coal tar–based mesophase (2.4 nm). Based on the identified features, the influence of the methyl group on the layering structures was investigated via molecular dynamics simulations. The results revealed that methyl groups are critical in mesophase layering in C-9 alkyl benzene- and naphthalene-based pitches, by reducing CH-π interaction. However, similar alignment could be achieved without the same degree of methyl substitutions for the coal tar-based pitch because of stronger π-π interaction than the other precursors. The insights from this study contribute to our understanding of the formation of conventional mesophase pitch and have implications for the processing of coal-derived materials. In conclusion, this knowledge is vital to produce valuable products like carbon fiber and graphite from pitches.

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

QuantumScents: Quantum-Mechanical Properties for 3.5k Olfactory Molecules

Quantitative structure–odor relationships are critically important for studies related to the function of olfaction. Current literature data sets contain expert-labeled molecules but lack feature data. This paper introduces QuantumScents, a quantum mechanics augmented derivative of the Leffingwell data set. QuantumScents contains 3.5k structurally and chemically diverse molecules ranging from 2 to 30 heavy atoms (CNOS) and their corresponding 3D coordinates, total PBE0 energy, molecular dipole moment, and per-atom Hirshfeld charges, dipoles, and ratios. The authors demonstrate that Hirshfeld charges and ratios contain sufficient information to perform molecular classification by training a Message Passing Neural Network with chemprop (Heid, E.; et al. ChemRxiv, 2023, DOI: 10.26434/chemrxiv-2023-3zcfl) to predict scent labels. Finally, the QuantumScents data set is freely available on Zenodo along with the authors’ code, example models, and data set generation workflow (https://zenodo.org/doi/10.5281/zenodo.8239853).

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

Cation-Induced Disruption of the Local Structure of Water in Faujasite

Here, the changes in the structure of water confined in faujasite were resolved by a series of ab initio molecular dynamic simulations of explicit water molecules in faujasite with varying Si/Al ratio and counterions present. Radial distribution functions of water oxygen atom pairs, as well as counterions to Al pairs, were calculated to quantify the structure of water in faujasite and the distribution of counterions in the water-filled faujasite pores. Radial distribution functions reveal that confinement without counterions results in more water molecules hydrogen bound to each other. In hydrogen-exchanged faujasite, the increase in aluminum content led to the disruption of the confined water structure as charge-compensating protons dissociated from Al tetrahedra and entered the liquid water in the pores. In addition, a potential of mean force of proton transfer shows that protons are thermodynamically favored to be in the liquid water rather than bound on Al tetrahedra. Exchanged Na + and La 3+ counterions, which remain closer to Al tetrahedra in liquid water than H + , also disordered the confined water structure. Two La 3+ ions disrupted water less than did six Na + ions, suggesting that, for the alkali and lanthanide ions, the number of counterions in FAU has a larger effect on the structure of water than the charge of the ion itself.

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

Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI

Abstract Type IIS restriction endonucleases contain separate DNA recognition and catalytic domains and cleave their substrates at well-defined distances outside their target sequences. They are employed in biotechnology for a variety of purposes, including the creation of gene-targeting zinc finger and TAL effector nucleases and DNA synthesis applications such as Golden Gate assembly. The most thoroughly studied Type IIS enzyme, FokI, has been shown to require multimerization and engagement with multiple DNA targets for optimal cleavage activity; however, details of how it or similar enzymes forms a DNA-bound reaction complex have not been described at atomic resolution. Here we describe biochemical analyses of DNA cleavage by the Type IIS PaqCI restriction endonuclease and a series of molecular structures in the presence and absence of multiple bound DNA targets. The enzyme displays a similar tetrameric organization of target recognition domains in the absence or presence of bound substrate, with a significant repositioning of endonuclease domains in a trapped DNA-bound complex that is poised to deliver the first of a series of double-strand breaks. PaqCI and FokI share similar structural mechanisms of DNA cleavage, but considerable differences in their domain organization and quaternary architecture, facilitating comparisons between distinct Type IIS enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

How does your gyroid grow? A mesoatomic perspective on supramolecular, soft matter network crystals

We propose and describe a framework to understand the structure of supramolecular network crystals formed in soft matter in terms of mesoatomic building blocks, collective groupings of amphiphilic molecules that play a role analogous to atomic or molecular subunits of hard matter crystals. While the concept of mesoatoms is intuitive and widely invoked in crystalline arrangements of spherelike or cylinderlike (micellelike) domains, analogous notions of natural and physically meaningful building blocks of triply periodic network (TPN) crystals, like the double-gyroid or double-diamond structures are obscured by the complex, bicontinuous domain shapes and intercatenated topologies of the double networks. Focusing on the specific example of diblock copolymer melts, we propose generic rules for decomposing TPN crystals into a unique set of mesoatomic building blocks. Based on physically motivated principles, the combination of symmetries and topologies of these structures point to mesoatomic elements associated with the nodal connections, leading to mesoatomic volumes that are nonconvex and bound by smoothly curved faces, unlike the more familiar Voronoi polyhedral shapes associated with spherelike and cylinderlike mesoatoms. We analyze the shapes of these mesoatoms, their internal structure, and importantly, their local packing with neighbor mesoatomic units. Importantly, we hypothesize that mesoatoms are kinetically favored intermediate structures whose local shapes and packing template network crystal assembly on long time scales. We propose and study a minimal energetic model of mesoatom assembly for three different cubic double-network crystals, based on local shape packing, which predicts a detailed picture for kinetics of intercatenation and surface growth. Based on these analyses, we discuss several possible extensions and elaborations of the mesoatomic description of supramolecular soft matter network crystals, most notably the implications of mesoatomic malleability, a feature that distinguishes soft matter from hard matter crystals. We describe experimental observations of malleable mesoatomic units in the precursor sponge phase as well as in ordered cubic networks and suggest possibilities for observing mesoatoms in primordial, precrystalline states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

The effects of stress, temperature and facet structure on growth of { 10 1 ¯ 2 } twins in Mg: a molecular dynamics and phase field study

The present study focuses on the roles of structure, stress and temperature on the mobility of facets bounding twin domains and on the overall impact on the growth kinetics of { 10 1 ¯ 2 } twins in Mg. We first use molecular dynamics simulations (MD) to study the relationship between interface structures, stress, temperature and mobility. As facets can exhibit distinct atomic scale structures, we also quantify the effect of stress relaxation mediated by misfit dislocations on the mobility of the basal-prismatic interface. The information gathered for ten different facets is used to calibrate an anisotropic phase field model predicting the effects of temperature and stress on the kinetics and shape of a growing { 10 1 ¯ 2 } 3D twin, by comparison with MD data. The comparative analysis suggests that, as compared to simulations of individual facets, the effective mobility of facets can be significantly different during growth of a 3D twin. This can be attributed to the complex three-dimensional internal stress state of the twin and to coupling in facet motion triggered by facet junctions. As such, by directly fitting both the twin growth kinetics and morphology as predicted by MD for different stresses and temperatures, we can identify a limited set of rate-limiting facets that control twin growth and morphology, and measure their effective mobility.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis

Proteins are allosteric machines that couple motions at distinct, often distant, sites to control biological function. Low-frequency structural vibrations are a mechanism of this long-distance connection and are often used computationally to predict correlations, but experimentally identifying the vibrations associated with specific motions has proved challenging. Spectroscopy is an ideal tool to explore these excitations, but measurements have been largely unable to identify important frequency bands. The result is at odds with some previous calculations and raises the question what methods could successfully characterize protein structural vibrations. Here we show the lack of spectral structure arises in part from the variations in protein structure as the protein samples the energy landscape. However, by averaging over the energy landscape as sampled using an aggregate 18.5 μs of all-atom molecular dynamics simulation of hen egg white lysozyme and normal-mode analyses, we find vibrations with large overlap with functional displacements are surprisingly concentrated in narrow frequency bands. These bands are not apparent in either the ensemble averaged vibrational density of states or isotropic absorption. However, in the case of the ensemble averaged anisotropic absorption, there is persistent spectral structure and overlap between this structure and the functional displacement frequency bands. We systematically lay out heuristics for calculating the spectra robustly, including the need for statistical sampling of the protein and inclusion of adequate water in the spectral calculation. The results show the congested spectrum of these complex molecules obscures important frequency bands associated with function and reveal a method to overcome this congestion by combining structurally sensitive spectroscopy with robust normal mode ensemble analysis.

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

A crossed molecular beams and computational study on the unusual reactivity of banana bonds of cyclopropane (c-C 3 H 6 ; X 1 A$^{'}_{1}$ ) through insertion by ground state carbon atoms (C( 3 P j ))

The mechanism and chemical dynamics of the reaction of ground electronic state atomic carbon C( 3 P j ) with cyclopropane c-C 3 H 6 (X 1 A$^{'}_{1}$) have been explored by combining crossed molecular beams experiments with electronic structure calculations of the pertinent triplet C 4 H 6 potential energy surface and statistical computations of product branching ratios under single-collision conditions. The experimental findings suggest that the reaction proceeds via indirect scattering dynamics through triplet C 4 H 6 reaction intermediate(s) leading to C 4 H 5 product(s) plus atomic hydrogen via a tight exit transition state, with the overall reaction exoergicity evaluated as 231 ± 52 kJ mol –1 . The calculations indicate that C( 3 P j ) can easily insert into one of the three equivalent C–C ‘banana’ bonds of cyclopropane overcoming a low barrier of only 2 kJ mol –1 following the formation of a van der Waals reactant complex stabilized by 15 kJ mol –1 . The carbon atom insertion into one of the six C–H bonds is also feasible via a slightly higher barrier of 5 kJ mol –1 . Here, these results highlight an unusual reactivity of cyclopropane's banana C–C bonds, which behave more like unsaturated C–C bonds with a π-character than saturated σ C–C bonds, which are known to be generally unreactive toward the ground electronic state atomic carbon such as in ethane (C 2 H 6 ). The statistical theory predicts the overall product branching ratios at the experimental collision energy as 50% for 1-butyn-4-yl, 33% for 1,3-butadien-2-yl, i-C 4 H 5 , and 11% for 1,3-butadien-1-yl, n-C 4 H 5 , with i-C 4 H 5 (230 kJ mol –1 below the reactants) favored by the C–C insertion providing the best match with the experimentally observed reaction exoergicity. The C( 3 P j ) + c-C 3 H 6 reaction is predicted to be a source of C 4 H 5 radicals under the conditions where its low entrance barriers can be overcome, such as in planetary atmospheres or in circumstellar envelopes but not in cold molecular clouds. Both i- and n-C 4 H 5 can further react with acetylene eventually producing the first aromatic ring and hence, the reaction of the atomic carbon with c-C 3 H 6 can be considered as an initial step toward the formation of benzene.

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

A coarse-grained model of clay colloidal aggregation and consolidation with explicit representation of the electrical double layer

The aggregation of clay minerals in liquid water exemplifies colloidal self-assembly in nature. These negatively charged aluminosilicate platelets interact through multiple mechanisms with different sensitivities to particle shape, surface charge, aqueous chemistry, and interparticle distance and exhibit complex aggregation structures. Experiments have difficulty resolving the associated colloidal assemblages at the scale of individual particles. Conversely, all-atom molecular dynamics (MD) simulations provide detailed insight on clay colloidal interaction mechanisms, but they are limited to systems containing a few particles. We develop a new coarse-grained (CG) model capable of representing assemblages of hundreds of clay particles with accuracy approaching that of MD simulations, at a fraction of the computational cost. Our CG model is parameterized based on MD simulations of a pair of smectite clay particles in liquid water. A distinctive feature of our model is that it explicitly represents the electrical double layer (EDL), i.e., the cloud of charge-compensating cations that surrounds the clay particles. Our model captures the simultaneous importance of long-range colloidal interactions (i.e., interactions consistent with simplified analytical models, already included in extant clay CG models) and short-range interactions such as ion correlation and surface and ion hydration effects. The resulting simulations correctly predict, at low solid-water ratios, the existence of ordered arrangements of parallel particles separated by water films with a thickness up to ~10 nm and, at high solid-water ratios, the coexistence of crystalline and osmotic swelling states, in agreement with experimental observations.

54 ENVIRONMENTAL SCIENCES↗