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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 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Amphiphile Organization in Organic Solutions: An Alternative Explanation for Small-Angle X-ray Scattering Features in Malonamide/Alkane Mixtures

In this work, the role of different intermolecular interactions in the aggregation of amphiphiles in an organic solvent is studied for systems of relevance to liquid-liquid extraction (LLE), a chemical process used to selectively recover metals from complex mixtures. Of specific interest is the role, or lack thereof, of hydrogen bonding, which is often assumed to be a main driver of the organic phase structural organization that has been linked to separation efficacy. Toward that end, a series of malonamide extractants in n-dodecane have been studied in the absence of any extracted aqueous solutes, including water. The series of extractants includes N,N'-dimethyl-N,N'-dibutyltetradecylmalonamide (DMDBTDMA), two of its homologs, and N,N'-dimethyl-N,N'-dioctylhexylethoxymalonamide (DMDOHEMA). This simplified model LLE system enables systematic investigation of the role of dipole-dipole and alkyl tail steric interactions in amphiphile aggregation. Small-angle X-ray scattering (SAXS) profiles computed from molecular dynamics trajectories are in good agreement with experimental SAXS data. Molecular dynamics simulations show that malonamide aggregation results from dipole-driven self-association and lacks characteristic aggregate sizes. Mid-q correlation peaks in the SAXS profiles emerge at high concentration for each malonamide. In those densely packed solutions, the correlation peaks are observed to result from alkyl tail-induced spacing between electron-rich polar head groups, with peak positions determined by the different alkyl tail lengths present in the malonamide molecule. This explanation of the SAXS correlation peaks contrasts with the prevailing literature, which attributes mesoscale features observed in small-angle scattering to the formation of microemulsions. Instead, this work finds that these features are present in the absence of water or any reverse micellar organization of the malonamides. As such, molecular-scale malonamide self-association and packing, rather than microemulsion-based colloidal-scale descriptions, is a more appropriate framework for these LLE systems.

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

Correlated Response of Protein Side-Chain Fluctuations and Conformational Entropy to Ligand Binding

The heterogeneous fast side-chain dynamics of proteins plays crucial roles in molecular recognition and binding. Site-specific NMR experiments quantify these motions by measuring the model-free order parameter (O axis 2 ) on a scale of 0 (most flexible) to 1 (least flexible) for each methyl-containing residue of proteins. In this work, we have examined ligand-induced variations in the fast side-chain dynamics and conformational entropy of calmodulin (CaM) using five different CaM–peptide complexes. O axis 2 of CaM in the ligand-free (O axis,U 2 ) and ligand-bound (O axis,B 2 ) states are calculated from molecular dynamics trajectories and conformational energy surfaces obtained using the adaptive biasing force (ABF) method. ΔO axis 2 = O axis,B 2 – O axis,U 2 follows a Gaussian-like unimodal distribution whose second moment is a potential indicator of the binding affinity of these complexes. The probability for the binding-induced O axis,U 2 → O axis,B 2 transition decreases with increasing magnitude of ΔO axis 2 , indicating that large flexibility changes are improbable for side chains of CaM after ligand binding. A linear correlation established between ΔOaxis2 and the conformational entropy change of the protein makes possible the determination of the conformational entropy of binding of protein–ligand complexes. The results not only underscore the functional importance of fast side-chain fluctuations but also highlight key motional and thermodynamic correlates of protein–ligand binding.

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

Modeling Liquid Water by Climbing up Jacob’s Ladder in Density Functional Theory Facilitated by Using Deep Neural Network Potentials

Within the framework of Kohn–Sham density functional theory (DFT), the ability to provide good predictions of water properties by employing a strongly constrained and appropriately normed (SCAN) functional has been extensively demonstrated in recent years. Here, we further advance the modeling of water by building a more accurate model on the fourth rung of Jacob’s ladder with the hybrid functional, SCAN0. In particular, we carry out both classical and Feynman path-integral molecular dynamics calculations of water with the SCAN0 functional and the isobaric–isothermal ensemble. To generate the equilibrated structure of water, a deep neural network potential is trained from the atomic potential energy surface based on ab initio data obtained from SCAN0 DFT calculations. For the electronic properties of water, a separate deep neural network potential is trained by using the Deep Wannier method based on the maximally localized Wannier functions of the equilibrated trajectory at the SCAN0 level. The structural, dynamic, and electric properties of water were analyzed. The hydrogen-bond structures, density, infrared spectra, diffusion coefficients, and dielectric constants of water, in the electronic ground state, are computed by using a large simulation box and long simulation time. For the properties involving electronic excitations, we apply the GW approximation within many-body perturbation theory to calculate the quasiparticle density of states and bandgap of water. Compared to the SCAN functional, mixing exact exchange mitigates the self-interaction error in the meta-generalized-gradient approximation and further softens liquid water toward the experimental direction. For most of the water properties, the SCAN0 functional shows a systematic improvement over the SCAN functional. However, some important discrepancies remain. The H-bond network predicted by the SCAN0 functional is still slightly overstructured compared to the experimental results.

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

Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures

Proteins have been found to inhabit a diverse set of three-dimensional structures. The dynamics that govern protein interconversion between structures happen over a wide range of time scales-picoseconds to seconds. Our understanding of protein functions and dynamics is largely reliant upon our ability to elucidate physically populated structures. From an experimental structural characterization perspective, we are often limited to measuring the ensemble-averaged structure both in the steady-state and time-resolved regimes. Generating kinetic models and understanding protein structure–function relationships require atomistic knowledge of the populated states in the ensemble. Here, we present ensemble refinement methodologies that integrate time-resolved experimental signals with molecular dynamics models. We first discuss integration of experimental structural restraints to molecular models in disordered protein systems that adhere to the principle of maximum entropy for creating a complete set of ensemble structures. We then propose strategies to find kinetic pathways between the refined structures, using time-resolved inputs to guide molecular dynamics trajectories and the use of inference to generate tailored stimuli to prepare a desired ensemble of protein states.

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

A Computational Study of RNA Tetraloop Thermodynamics, Including Misfolded States

An important characteristic of RNA folding is the adoption of alternative configurations of similar stability, often referred to as misfolded configurations. These configurations are considered to compete with correctly folded configurations, although their rigorous thermodynamic and structural characterization remains elusive. Tetraloop motifs found in large ribozymes are ideal systems for an atomistically detailed computational quantification of folding free energy landscapes and the structural characterization of their constituent free energy basins, including nonnative states. In this work, we studied a group of closely related 10-mer tetraloops using a combined parallel tempering and metadynamics technique that allows a reliable sampling of the free energy landscapes, requiring only knowledge that the stem folds into a canonical A-RNA configuration. Here we isolated and analyzed unfolded, folded, and misfolded populations that correspond to different free energy basins. We identified a distinct misfolded state that has a stability very close to that of the correctly folded state. This misfolded state contains a predominant population that shares the same structural features across all tetraloops studied here and lacks the noncanonical A-G base pair in its loop portion. Further analysis performed with biased trajectories showed that although this competitive misfolded state is not an essential intermediate, it is visited in most of the transitions from unfolded to correctly folded states. Moreover, the tetraloops can transition from this misfolded state to the correctly folded state without requiring extensive unfolding.

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

Insights into Sorption and Molecular Transport of Aqueous Glucose into Zeolite Nanopores

Liquid-phase heterogeneous catalysis using zeolites is important for biomass conversion to fuels and chemicals. There is a substantial body of work on gas-phase sorption in zeolites with different topologies; however, studies investigating the diffusion of complex molecules in liquid medium into zeolitic nanopores are scarce. Here, we present a molecular dynamics study to understand the sorption and diffusion of aqueous β-d-glucose into β-zeolite silicate at T = 395 K and P = 1 bar. Through 2-μs-long molecular dynamics trajectories, we reveal the role of the solvent, the kinetics of the pore filling, and the effect of the water model on these properties. We find that the glucose and water loading is a function of the initial glucose concentration. Although the glucose concentration increases monotonically with the initial glucose concentration, the water loading exhibits a nonmonotonic behavior. At the highest initial concentration (~20 wt %), we find that the equilibrium loading of glucose is approximately five molecules per unit cell and displays a weak dependence on the water model. Glucose molecules follow a single-file diffusion in the nanopores due to confinement. Here, the dynamics of glucose and water molecules slows significantly at the interface. The average residence time for glucose molecules is an order of magnitude larger than that in the bulk solution, while it is about twice as large for the water molecules. Our simulations reveal critical molecular details of the glucose molecule’s local environment inside the zeolite pore relevant to catalytic conversion of biomass to valuable chemicals.

09 BIOMASS FUELS↗
DOE OSTI2024

Time-Resolved X-ray Emission Spectroscopy and Resonant Inelastic X-ray Scattering Spectroscopy of Laser Irradiated Carbon

The existence of liquid carbon as an intermediate phase preceding the formation of novel carbon materials has been a point of contention for several decades. Experimental observation of such a liquid state requires nonthermal melting of solid carbon materials at various laser fluences and pulse properties. Reflectivity experiments performed in the mid-1980s reached opposing conclusions regarding the metallic or insulating properties of the purported liquid state. Time-resolved X-ray absorption studies showed shortening of C–C bonds and increasing diffraction densities, thought to evidence a liquid or glassy carbon state, respectively. Nevertheless, none of these experiments provided information on the electronic structure of the proposed liquid state. Herein, we report the results of time-resolved resonant inelastic X-ray scattering (RIXS) and time-resolved X-ray emission spectroscopy (XES) studies on amorphous carbon (a-C) and ultrananocrystalline diamond (UNCD) as a function of delay time between the irradiating pulse and X-ray probe. For both a-C and UNCD, we attribute decreases in RIXS or XES signals to transition blocking, relaxation, and finally, ablation. Increased signal at 20 ps following the irradiation of the UNCD is attributed to the probable formation of nanoscale structures in the ablation plume. Further, differences in the amount of signal observed between a-C and UNCD are explained by the difference in sample thickness and, specifically, incomplete melting of the UNCD film. Comparisons to spectral simulations based on MD trajectories at extreme conditions indicate that the carbon state in our experiments is crystalline. Normal mode analysis confirmed that symmetrical bending or stretching of the C–C bonds in the diamond lattice results in XES spectra with small intensity differences. Overall, we observed no evidence of melting to a liquid state, as determined by the lack of changes in the spectral properties for up to 100 ps delays following the melting pulses.

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

The Potential Energy Hotspot: Effects of Impact Velocity, Defect Geometry, and Crystallographic Orientation

In energetic materials, the localization of energy into “hotspots” is known to dictate the initiation of chemical reactions and detonation. Recent all-atom simulations have shown that more energy is localized as internal potential energy (PE) than can be inferred from the kinetic energy (KE) alone. The mechanisms associated with pore collapse and hotspot formation are known to depend on pore geometry and dynamic material response such as plasticity. Therefore, we use molecular dynamics (MD) simulations to characterize shock-induced pore collapse and the subsequent formation of hotspots in 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a highly anisotropic molecular crystal, for various defect shapes, shock strengths, and crystallographic orientations. We find that the localization of energy as PE is consistently larger than the KE in cases with significant plastic deformation. Additionally, an analysis of MD trajectories reveals the underlying molecular- and crystal-level processes that govern the effect of orientation and pore shape on PE localization. We find that the regions of highest PE relate to the areas of maximum plastic deformation, while KE is maximized at the point of impact. Comparisons against octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) reveal less energy localization in TATB, which could be a contributing factor to the latter’s insensitivity.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Low-Energy Ion Scattering Intensities from Supported Nanoparticles: The Spherical Cap Model

Supported nanoparticles are of great importance to many technologies like fuel processing and chemical synthesis using catalysts and electrocatalysts, energy storage and generation using fuel cells and batteries, electrochemistry, magnetic information storage, and more. Low-energy ion scattering spectroscopy (LEIS) with noble gas ions like He+ is a powerful tool for the characterization of nanoparticles dispersed across flat support surfaces due to its ability to probe the elemental composition in the topmost atomic layer of a surface, providing quantitative information regarding the size and number density of nanoparticles. In this work, we present a derivation of the LEIS intensities expected from nanoparticles and the support material as a function of the average particle size, their number per unit area, and their contact angle with the support when modeled as spherical caps of the nanoparticle material dispersed over the surface of a flat support. The model assumes that the ion intensities are determined only by the physical blocking of linear ion trajectories and independent of the tilt angle of the local surface relative to the incident and scattered ion directions, an assumption we support by quantitative modeling of published data which tested tilt-angle effects. The model is a generalization to arbitrary contact angles of the hemispherical cap model, which assumes 90° contact angle and has been widely used to model spectroscopic signals in LEIS (and also in Auger and photoelectron spectroscopies) during nanoparticle growth. Here, this new model quantitatively reveals how LEIS signals are sensitive not only to the diameter and number density of the nanoparticle but also to their contact angle (or height/diameter ratio). With the use of additional data (e.g., from microscopy or adsorption microcalorimetry), the model presented here will enable more accurate determination of the average size, shape, and number density of supported nanoparticles based on LEIS intensity measurements.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

Decoding the Pair Distribution Function of Uranium in Molten Fluoride Salts from X-Ray Absorption Spectroscopy Data by Machine Learning

Thermal properties of actinides in molten salts are linked to the strongly disordered local environment of actinide ions. Here, we illustrate both the limitations of the commonly used fitting method for analysis of extended X-ray absorption fine structure (EXAFS) spectra in molten UF 4 and a possible solution using an "objective neural network - EXAFS" (ONNE) method. ONNE provides both extraction of the pair distribution function, as validated by its application to the EXAFS spectra calculated on molecular dynamics trajectory, and the EXAFS data reconstruction. The ONNE analysis of the molten UF4 has revealed reduction of the first nearest neighbor U-F coordination number, expansion of the U-F bond length and smaller contribution to the second shell compared to its crystalline counterpart. This method is therefore an attractive alternative to conventional EXAFS analysis and molecular dynamics simulations for studies of disordered environment of actinides in molten salts.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Excitons in Hematite Fe 2 O 3 : Short-Time Dynamics from TD-DFT and Non-Adiabatic Dynamics Theories

We present a first-principles study of the short-time dynamics of excitons in hematite Fe 2 O 3 . We used time-dependent density functional theory (TD-DFT) with an underlying DFT+U treatment of electron interactions to characterize the electronic structure of excitons and nonadiabatic molecular dynamics theory (NA-MD) to determine their recombination (electronic ground-state recovery) and relaxation dynamics. Decoherence-corrected trajectory surface hopping approaches in NA-MD simulations yielded recovery times of ~1.1 to 1.8 ns and “higher-lying” exciton relaxation times of ~60 to 70 fs, in accord with experimentally derived lifetimes. With hematite phonons in the range of ~100 to 700 cm –1 , higher-lying excitons relax within one or two oscillations of the phonons before getting trapped into an electron–hole pair Exc-3 structure on the first excited state potential energy surface. This structure resembles already a pair of polarons (electron polaron plus hole polaron) with associated lattice distortions three (3) basal planes away. On longer time scales, the electron–hole bipolaronic pair hops to structures Exc-5, then Exc-7, then Exc-9, ... with the electron polaron and hole polaron separated by 5, 7, 9, ... basal planes in a process of charge separation. The largest frequency phonon ~672 cm –1 for the Exc-3 exciton structure is associated with the electron polaron moiety of the exciton. This phonon is a good candidate for giving rise to the recently observed and reported postexcitation transient IR absorption peak.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Machine-Learned Force Field for Molecular Dynamics Simulations of Nonequilibrium Ammonia Synthesis on Iron Catalysts

Ammonia (NH 3 ) is one of the most important industrial chemicals. The conventional NH 3 synthesis method-the Haber–Bosch process-converts atmospheric nitrogen (N 2 ) into NH 3 using H 2 with an iron (Fe) catalyst. However, this process requires high pressures (100–200 atm) and temperatures (700–800 K) near thermal equilibrium. Recently, Fe-based nanocatalysts have been reported to produce promising NH 3 yields under atmospheric pressures and temperature-modulated nonequilibrium conditions. Understanding the mechanism of nonequilibrium catalysis with programmed temperature variation could help to optimize this fully electrified and less energy-intensive process. Although reactive molecular dynamics (RMD) simulations can be a useful tool to model nonequilibrium catalytic processes, they require the development of accurate force fields (i.e., interatomic potentials). Here, we present a machine-learned (ML) force field within the Deep Potential MD (DPMD) framework, trained using periodic density functional theory (DFT) calculations, to model NH 3 synthesis on Fe catalysts with various surface adsorbates such as *N, *H, *N 2 , *H 2 , *NH, *NH 2 , and *NH 3 . Here, we generated the DFT data from static models of elementary reactions on the most stable (110) surface of body-centered cubic Fe, which then were augmented by data from constant number of particles–volume–temperature (NVT) DFT-MD trajectories at various temperatures. Finally, we utilized the fully optimized ML force field to investigate reaction dynamics at an Fe(110) surface at linearly increasing temperatures using NVT-DPMD simulations. Our simulations indicate that pulsed temperature ramping could prove favorable for NH3 synthesis. For example, we conducted ramping under multiple sets of conditions: (i) from 900 to 1200 K over periods of 0.1–0.3 ns for Fe surfaces precovered with N or NH along with H; and (ii) from 300 to 600 K over 0.1–0.3 ns for Fe surfaces precovered with NH 3 . While our simulations so far are limited to short time scales (very rapid heating), these observations shed light on the mechanism of the high NH 3 synthesis rate achieved in a novel temperature-modulated nonequilibrium catalytic reactor using pulsed heating and cooling.

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

Non-Adiabatic Excited State Molecular Dynamics Methodologies: comparison and convergence

Direct atomistic simulation of nonadiabatic molecular dynamics is a challenging goal that allows important insights into fundamental physical phenomena. A variety of frameworks, ranging from fully quantum treatment of nuclei to semiclassical and mixed quantum–classical approaches, were developed. These algorithms are then coupled to specific electronic structure techniques. Such diversity and lack of standardized implementation make it difficult to compare the performance of different methodologies when treating realistic systems. Here, we compare three popular methods for large chromophores: Ehrenfest, surface hopping, and multiconfigurational Ehrenfest with ab initio multiple cloning (MCE-AIMC). These approaches are implemented in the NEXMD software, which features a common computational chemistry model. The resulting comparisons reveal the method performance for population relaxation and coherent vibronic dynamics. Finally, we study the numerical convergence of MCE-AIMC algorithms by considering the number of trajectories, cloning thresholds, and Gaussian wavepacket width. Our results provide helpful reference data for selecting an optimal methodology for simulating excited-state molecular dynamics.

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

Magnetic-Field-Driven Electron Dynamics in Graphene

Graphene exhibits unique optoelectronic properties originating from the band structure at the Dirac points. It is an ideal model structure to study the electronic and optical properties under the influence of the applied magnetic field. In graphene, electric field, laser pulse, and voltage can create electron dynamics which is influenced by momentum dispersion. However, computational modeling of momentum-influenced electron dynamics under the applied magnetic field remains challenging. In this work, we perform computational modeling of the photoexcited electron dynamics achieved in graphene under an applied magnetic field. Our results show that magnetic field leads to local deviation from momentum conservation for charge carriers. With the increasing magnetic field, the delocalization of electron probability distribution increases and forms a cyclotron-like trajectory. Our work facilitates understanding of momentum resolved magnetic field effect on non-equilibrium properties of graphene, which is critical for optoelectronic and photovoltaic applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2

SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine learning (ML), and free-energy perturbation (FEP) calculations to elucidate the differences in binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD–ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Extemporaneous Mechanochemistry: Shock-Wave-Induced Ultrafast Chemical Reactions Due to Intramolecular Strain Energy

We report regions of energy localization referred to as hotspots are known to govern shock initiation and the run-to-detonation in energetic materials. Mounting computational evidence points to accelerated chemistry in hotspots from large intramolecular strains induced via the interactions between the shock wave and microstructure. However, definite evidence mapping intramolecular strain to accelerated or altered chemical reactions has so far been elusive. From a large-scale reactive molecular dynamics simulation of the energetic material 1,3,5-triamino-2,4,6-trinitrobenzene, we map decomposition kinetics to molecular temperature and intramolecular strain energy prior to reaction. Both temperature and intramolecular strain are shown to accelerate chemical kinetics. A detailed analysis of the atomistic trajectory shows that intramolecular strain can induce a mechanochemical alteration of decomposition mechanisms. The results in this paper could inform continuum-level chemistry models to account for a wide range of mechanochemical effects.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The Surprising Dynamics of the McLafferty Rearrangement

We report femtosecond time-resolved measurements of the McLafferty rearrange- ment following the strong-field tunnel ionization of 2-pentanone, 4-methyl-2-pentanone, and 4,4- dimethyl-2-pentanone. The pump–probe-dependent yields of the McLafferty product ion are fit to a biexponential function with fast (~100 fs) and slow (~10 ps) time constants, the latter of which is faster for the latter two compounds. Following nearly instantaneous ionization, the fast time scale is associated with rotation of the molecule to a six-membered cyclic intermediate that facilitates transfer of the γ-hydrogen, while the ~50–100 times longer time scale is associated with a π-bond rearrangement and bond cleavage between the α- and β-carbons to produce the enol cation. Furthermore, these experimental measurements are supported by ab initio molecular dynamics trajectories, which further confirm the time scale of this important stepwise reaction in mass spectrometry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗