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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
NASA NTRS1998

Energetics and Dynamics of GaAs Epitaxial Growth via Quantum Wave Packet Studies

The dynamics of As(sub 2) molecule incorporation into the flat Ga-terminated GaAs(100) surface is studied computationally. The time-dependent Schrodinger equation is solved on a two-dimensional potential energy surface obtained using density functional theory calculations. The probabilities of trapping and subsequent dissociation of the molecular As(sub 2) bond are calculated as a function of beam translational energy and vibrational quantum number of As(sub 2).

Dzegilenko, Fedor N.↗
NASA NTRS1993

Modeling study on the cleavage step of the self-splicing reaction in group I introns

A three-dimensional model of the Tetrahymena thermophila group I intron is used to further explore the catalytic mechanism of the transphosphorylation reaction of the cleavage step. Based on the coordinates of the catalytic core model proposed by Michel and Westhof (Michel, F., Westhof, E. J. Mol. Biol. 216, 585-610 (1990)), we first converted their ligation step model into a model of the cleavage step by the substitution of several bases and the removal of helix P9. Next, an attempt to place a trigonal bipyramidal transition state model in the active site revealed that this modified model for the cleavage step could not accommodate the transition state due to insufficient space. A lowering of P1 helix relative to surrounding helices provided the additional space required. Simultaneously, it provided a better starting geometry to model the molecular contacts proposed by Pyle et al. (Pyle, A. M., Murphy, F. L., Cech, T. R. Nature 358, 123-128. (1992)), based on mutational studies involving the J8/7 segment. Two hydrated Mg2+ complexes were placed in the active site of the ribozyme model, using the crystal structure of the functionally similar Klenow fragment (Beese, L.S., Steitz, T.A. EMBO J. 10, 25-33 (1991)) as a guide. The presence of two metal ions in the active site of the intron differs from previous models, which incorporate one metal ion in the catalytic site to fulfill the postulated roles of Mg2+ in catalysis. The reaction profile is simulated based on a trigonal bipyramidal transition state, and the role of the hydrated Mg2+ complexes in catalysis is further explored using molecular orbital calculations.

NASA Discipline Exobiology↗
DOE OSTI2025

Elucidation of an Unusually Long Pu–N Bond in a Plutonium(III)-Tetrazolate Complex

Four trivalent, f-element tetrazolate hydrate complexes [M(H 2 O) 9 ](Hdtb) 3 ·nH 2 O (Nd1, n = 7 and Pu1, n = 9; dtb 2– = 1,3-di(tetrazolate-5-yl)benzene) and [M(Hdtb)(H 2 O) 8 ](dtb)·11H 2 O (Nd2 and Pu2) were prepared using metathesis reactions. These complexes contain hydrated M(III) cations, but in the latter complexes, Nd2 and Pu2, one of the water molecules has been displaced by a long interaction between the M(III) cation and a Hdtb – anion. Notably, the Pu(III)–N bond in Pu2, representing the longest IX Pu(III)–N ( IX = nine coordinate) bond reported has a length of 2.8338(15) Å and is slightly shorter than the Nd(III)–N bond length of 2.8425(13) Å in Nd2. Analysis of bond lengths, Wiberg bond indices (WBI), natural localized molecular orbitals (NLMOs), and quantum theory of atoms in molecules (QTAIM) reveals that the metal contribution to the Pu(III)–N bond is marginally greater than that of the Pu(III)–OH 2 bonds in Pu2 and the Nd(III)–N bond in Nd2. Thus, this rather long M–N interaction provides an example where the expectation that An(III) compounds exhibit greater covalency with soft donor ligands compared to harder ligands fails. Furthermore, the absorption spectra of Pu1 and Pu2 further support this observation, highlighting a surprising degree of similarity in their electronic structures.

Covalent bonding↗
DOE OSTI2023

Roles of Hydrogen Bonds and Alignment in Oriented Attachment of Gibbsite Nanoparticles: Insights from Molecular Dynamics

Oriented attachment (OA) of nanoparticles is an important crystal growth pathway in the synthesis of hierarchical structures. Although a significant understanding of OA has been made, the effect of atomistic misalignment and the roles of solvent/particle and particle/particle interactions on the structure–energy relationship during an OA remain elusive. In this study, we perform molecular dynamics simulations to calculate the potential of mean force (PMF) profile for gibbsite particle translation on a gibbsite slab with 1 or 2 intervening water layers (1W or 2W). The structures of the gibbsite surfaces and the confined water are analyzed to determine how the number and type of hydrogen bonds (H-bonds) influence the free energy profile during the translation. The PMF profile exhibits a periodicity of length 5.078 Å, consistent with the gibbsite unit cell size along the translation direction. The changes in the surface–water and water–water hydrogen bond network and water and surface OH groups’ orientations during the translation are strongly coupled with the changes in the PMF profile in the 1W case. However, when increasing the number of intervening water layers from 1W to 2W, the particle/slab misalignment becomes a dominant factor controlling the behavior of the PMF profile. We also establish a method to quantify misalignment between the particle and the slab, which exhibits a strong correlation with the free energy for the 2W case. These results shed more light into the roles of particle/slab misalignment and hydrogen bond network in the OA of mineral particles in aqueous solution.

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

Spectroscopic Probe Molecule Selection Using Quantum Theory, First-Principles Calculations, and Machine Learning

Probe molecule vibrational spectra have a long history of being used to characterize materials including metals, oxides, metal-organic frameworks, and even human proteins. Furthermore, recent advances in machine learning have enabled computationally generated spectra to aid in detailed characterization of complex surfaces with probe molecules. Despite widespread use of probe molecules, the science of probe molecule selection is underdeveloped. Here, we develop physical concepts, including orbital interaction energy and the energy overlap integral, to explain and predict the ability of probe molecules to discriminate structural descriptors. We resolve the crystal orbital overlap population (COOP) to specific molecular orbitals and quantify their bonding character, which directly influences vibrational frequencies. Using only a single adsorbate calculation from density function theory (DFT), we compute the interaction energy of individual adsorbate molecular orbitals with adsorption site atomic orbitals across many different sites. Combining the molecular orbital resolved COOP and changes in orbital interaction energy enables probe molecule selection for improved discrimination of various sites. We demonstrate these concepts by comparing the predicted effectiveness of carbon monoxide (CO), nitric oxide (NO), and ethylene (C 2 H 4 ) to probe Pt adsorption sites. Finally, using a previously developed machine learning framework, we show that models trained on hundreds of thousand C 2 H 4 spectra, computed from DFT, which regress surface binding-type and generalized coordination number (GCN), outperform those trained using CO and NO spectra. Lastly, a python package, pDOS_overlap, for implementing the electron density based analysis on any combination of adsorbates and materials, is also made available.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
NASA NTRS1992

Polyimide molding powder, coating, adhesive, and matrix resin

The invention is a polyimide prepared from 3,4'-oxydianiline (3,4'-ODA) and 4,4'-oxydiphthalic anhydride (ODPA), in 2-methoxyethyl ether (diglyme). The polymer was prepared in ultra high molecular weight and in a controlled molecular weight form which has a 2.5 percent offset in stoichiometry (excess diamine) with a 5.0 percent level of phthalic anhydride as an endcap. This controlled molecular weight form allows for greatly improved processing of the polymer for moldings, adhesive bonding, and composite fabrication. The higher molecular weight version affords tougher films and coatings. The overall polymer structure groups in the dianhydride, the diamine, and a metal linkage in the diamine affords adequate flow properties for making this polymer useful as a molding powder, adhesive, and matrix resin.

St.clair, Terry L.↗
DOE OSTI2022

Hydrogen-Bond-Promoted Planar Conformation, Crystallinity, and Charge Transport in Semiconducting Diazaisoindigo Derivatives

Conformational control of π-conjugated molecules using intramolecular noncovalent bonds represents a promising strategy to tailor the solid-state molecular packing and electronic properties of these materials. Here, we report the design and synthesis of two model compounds featuring intramolecular hydrogen bonds formed between a center diazaisoindigo unit (the acceptor) and flanking indole units (the donor). Computational and experimental investigations show that these hydrogen bonds enthalpically stabilize the coplanar molecular conformation by over 10 kcal/mol. The formation of these hydrogen bonds is also slightly favorable in terms of entropy, ensuring high temperature stability of the planar conformation. In this work, thermal annealing of thin films of these compounds imparts high crystallinity and orientation in the solid state, while the non-hydrogen bond control only gave an amorphous solid. Field-effect transistor devices fabricated from these thin films exhibit hole mobilities up to 0.270 cm 2 V -1 s -1 , in contrast to the lack of measurable charge carrier mobility for the non-hydrogen bond control. This work demonstrates an efficient synthetic strategy to incorporate robust intramolecular hydrogen bonds into conjugated π-systems and elucidates the mechanism on how such hydrogen bonds promote the desired molecular conformation, solid-state packing, and electronic performances of conjugated organic materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Large-scale atomistic model construction of subbituminous and bituminous coals for solvent extraction simulations with reactive molecular dynamics

Large-scale atomistic models for complex polycyclic aromatic hydrocarbon systems help understand the chemical properties and behaviors of complex feedstocks such as coal or petroleum. However, the development and utilization of large-scale models remain limited due to the difficulty in achieving the varied structural characteristics necessary to capture stochastic nature of these feedstocks. Here we demonstrate a systematic workflow to construct stochastic molecular systems from a broad analytical suite: high-resolution transmission electron microscopy (HRTEM), carbon-13 nuclear magnetic resonance spectroscopy ( 13 C NMR), laser desorption ionization mass spectroscopy (LDI-MS), and elemental analysis. We present a model construction and analysis utility of a new Python-based module. We selected one subbituminous and three high-volatile bituminous coals to construct large-scale models (~40,000 atoms). The constructed models were utilized to examine the affinity for solvent extraction (naphthalene or tetralin) and the effect of structural properties (e.g., aromatic cluster size, functional groups, and cross-linking) in reactive molecular dynamics simulations. Complex chemical reactions were monitored with bond order transitions, intermediates formation, and mass distributions. Reactive molecular dynamics simulations suggest a plausible chemical extraction process and products for the complex fossil feedstocks. The results indicated that radical formations with bond breaking of bridging oxygens and carbons were required at high temperatures to facilitate hydrogeneration and extraction of gas molecules from radical-free molecules. We observed that aliphatic chains of tetralin were easily decomposed and combined with radicals to form small size of molecules with aryl bonding, mainly increasing molecules in the 500–1000 Da, while naphthalene had little impact on chemical extraction process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Isolating solvent–solute hydrogen bonding interactions via 2D IR solvation shell spectroscopy

The solvation shell around a solute is a fundamental feature of liquid-phase solutions, determining the behavior and properties of both the solute and the overall solution. Direct experimental measurements of the solvation shell properties are challenging due to the strong signals generated from the bulk solvent, which overwhelm the small contribution of the solvation shell. Here, we use ultrafast two dimensional infrared (2D IR) spectroscopy and intermolecular cross-peaks to isolate the IR absorption spectrum of methanol molecules in the solvation shell surrounding the solute N-methylacetamide. We demonstrate that the intermolecular coupling between the solvent and solute vibrations is indirectly mediated by a low-frequency hydrogen-bonding mode, suggesting an important mechanism for anharmonic coupling induced by hydrogen bonds. From the relative frequency shifts and cross-peak anisotropy, we find that methanol molecules surrounding N-methylacetamide form stronger and distinctly oriented hydrogen bonds than those in the bulk solvent. Here, we also compare these results with the solvent spectra of the solute N,N-dimethylacetamide to investigate how solute structural changes alter the solvation shell and the contribution of N–H hydrogen bond donation. Our results are supported by molecular dynamics simulations, which provide detailed insights into the hydrogen-bonding distributions. Through these results, we demonstrate 2D solvation shell spectroscopy to be a valuable method for investigating solvation structures and dynamics without interference from the bulk solvent.

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

Controlling the toxicity of biomass-derived difunctional molecules as potential pharmaceutical ingredients for specific activity toward microorganisms and mammalian cells

A biomass-derived difuran compound, denoted as HAH (HMF–acetone–HMF), synthesized by aldol-condensation of 5-hydroxyfurfural (HMF) and acetone, can be partially hydrogenated to provide an electron-rich difuran compound (PHAH) for Diels–Alder reactions with maleimide derivatives. The nitrogen (N) site in the maleimide can be substituted by imidation with amine-containing compounds to control the hydrophobicity of the maleimide moiety in adducts of furans and maleimide by Diels–Alder reaction, denoted as norcantharimides (Diels–Alder adducts). The structural effects on the toxicity of various biomass-derived small molecules synthesized in this manner to regulate biological processes, defined as low molecular weight (≤1000 g mol -1 ) organic compounds, were investigated against diverse microbial and mammalian cell types. The biological toxicity increased when hydrophobic N-substitutions and C[double bond, length as m-dash]C bonds were introduced into the molecular structure. Among the synthesized norcantharamide derivatives, some compounds demonstrated pH-dependent toxicities against specific cell types. Reaction kinetics analyses of the norcantharimides in biological conditions suggest that this pH-dependent toxicity of norcantharimides could arise from retro Diels–Alder reactions in the presence of a Brønsted acid that catalyzes the release of an N-substituted maleimide, which has higher toxicity against fungal cells than the toxicity of the Diels–Alder adduct. These synthetic approaches can be used to design biologically-active small molecules that exhibit selective toxicity against various cell types (e.g., fungal, cancer cells) and provide a sustainable platform for production of prodrugs that could actively or passively affect the viability of infectious cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Machine learning-accelerated path integral molecular dynamics simulations of reactive organic electrolytes

Hydrogen bonded electrolytes that exhibit accelerated proton transport via sequential reactive hops have drawn interest for their promise in clean energy applications. Molecular dynamics simulations of these electrolytes offer the opportunity to uncover microscopic mechanistic details that could be used to design and tune the properties of candidate electrolyte technologies. However, accurately modeling the proton transfer reactions and transport properties that give rise to high charge conductivites in these electrolytes proves computationally challenging because of the need to perform lengthy condensed phase simulations, treating both the electronic and nuclear degrees of freedom quantum mechanically. In this paper, we demonstrate that such a modeling task can be efficiently achieved with the use of density functional theory (DFT)-trained machine learning potentials (MLP) to accelerate path integral molecular dynamics (PIMD) simulations. We highlight the practical utility of this approach by using it to benchmark how closely PIMD simulations employing different DFT exchange–correlation functionals reproduce the composition-dependent densities, diffusion coefficients, and electrical conductivities of mixtures consisting of imidazole and levulinic acid. Even with the speedup afforded by our MLPs, PIMD simulations remain quite expensive. Furthermore, in order to render PIMD more computationally tractable, we introduce and benchmark the accuracy of a ring polymer contraction approach that leverages a computationally efficient short-range MLP to accelerate our PIMD simulations by an additional factor of four.

Chemical bonding↗
DOE OSTI2023

Dinickel-Catalyzed N═N Bond Rotation

Azoarenes function as molecular switches that can be triggered by external stimuli, such as heat, light, and electrochemical potential. Here, in this work, we show that a dinickel catalyst can induce cis/trans isomerization in azoarenes through a N═N bond rotation mechanism. Catalytic intermediates containing azoarenes bound in both the cis and trans forms are characterized. Solid-state structures reveal the importance of π-back-bonding interactions from the dinickel active site in lowering the N═N bond order and accelerating bond rotation. The scope of the catalytic isomerization includes high-performance acyclic, cyclic, and polymeric azoarene switches.

adducts↗
DOE OSTI2021

Molecular coupling competing with defects within insulator of the magnetic tunnel junction-based molecular spintronics devices

Nearly 70 years old dream of incorporating molecule as the device element is still challenged by competing defects in almost every experimentally tested molecular device approach. This paper focuses on the magnetic tunnel junction (MTJ) based molecular spintronics device (MTJMSD) method. An MTJMSD utilizes a tunnel barrier to ensure a robust and mass-producible physical gap between two ferromagnetic electrodes. MTJMSD approach may benefit from MTJ's industrial practices; however, the MTJMSD approach still needs to overcome additional challenges arising from the inclusion of magnetic molecules in conjunction with competing defects. Molecular device channels are covalently bonded between two ferromagnets across the insulating barrier. An insulating barrier may possess a variety of potential defects arising during the fabrication or operational phase. This paper describes an experimental and theoretical study of molecular coupling between ferromagnets in the presence of the competing coupling via an insulating tunnel barrier. We discuss the experimental observations of hillocks and pinhole-type defects producing inter-layer coupling that compete with molecular device elements. We performed theoretical simulations to encompass a wide range of competition between molecules and defects. Monte Carlo Simulation (MCS) was used for investigating the defect-induced inter-layer coupling on MTJMSD. Our research may help understand and design molecular spintronics devices utilizing various insulating spacers such as aluminum oxide (AlOx) and magnesium oxide (MgO) on a wide range of metal electrodes. This paper intends to provide practical insights for researchers intending to investigate the molecular device properties via the MTJMSD approach and do not have a background in magnetic tunnel junction fabrication.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Ultrafast x-ray imaging of coherently controlled molecular dynamics in real space and time

Coherent control aims to manipulate chemical processes on the latent length and timescales of atoms and bonds, scales that are intrinsic to molecular dynamics but not directly resolved by most experimental probes. As a result, existing coherent-control experiments, which overwhelmingly rely on spectroscopic observables, leave a crucial blind spot: the direct, real-space recovery of all atomic and molecular rearrangements in response to coherently controlled excitations. Here, we overcome this limitation by integrating a Tannor-Kosloff-Rice pump-control-probe scheme with ultrafast X-ray scattering to capture snapshots of the wavepacket motion in a benchmark molecular system. We demonstrate this by photoexciting diatomic iodine vapor with a visible pump pulse, selectively steering the wavepacket toward ground-state recombination or dissociative pathways with a time-delayed near-IR control pulse, and recording the dynamics with angstrom and femtosecond precision with an ultrashort hard X-ray probe pulse. By comparing these structural observations with numerical solutions of the time-dependent Schrödinger equation, we reveal how coherent control actively reshapes the molecular charge density distribution. Our results pave the way for leveraging structural feedback as a control handle and provide a fundamental microscopic visualization of quantum decoherence and energy redistribution at the atomic level.

Hopper, Thomas R. [SLAC National Accelerator Labor↗
DOE OSTI2024

Use of Renewable Alcohols in Autocatalytic Production of Aspen Organosolv Lignins

This study aimed to investigate the intrinsic efficiency of renewable alcohols, applied under autocatalytic conditions, for removing lignin from aspen and hot-water-extracted aspen while substantially preserving the lignin structure so as to facilitate various valorization strategies. Ethylene glycol (EG), propylene glycol (PG), 1,4-butanediol (BDO), ethanol (EtOH), and tetrahydrofurfuryl alcohol (THFA) were evaluated based on their lignin solubilization ability, expressed as the relative energy difference (RED) following the principles of the Hansen solubility theory. The findings indicate that alcohols with a higher lignin solubilization potential lead to increased delignification, almost 90%, and produce a lignin with a higher content of β-O-4 bonds, up to 68% of those found in aspen milled wood lignin, thereby indicating their potential for valorization through depolymerization. However, these alcohols also produce lignin with a higher content of β-β and β-5 bonds, resulting in a higher molecular weight and polydispersity, due to readily occurring homolytic reactions. Hot-water extraction (HWE) conducted prior to alcohol treatment reduced the delignification efficiency and resulted in a lignin with a lower β-O-4 bond content. The lignins produced in these experiments exhibited a superior UV-A absorption capacity compared with synthetic benzophenone, as well as a greater radical quenching ability than synthetic butylated hydroxytoluene, indicating their potential for use in the protection of polymers against degradation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A Permanently Porous Chalcogen-Bonded Organic Framework

The nature of connectivity between constituent atomic or molecular building blocks is fundamental in shaping the properties and functionality of materials. The extrapolation of emergent interatomic interactions to enable functional materials has driven transformative technological advancements. However, the bonding interactions used in material design have been largely static since the emergence of dynamic covalent chemistry ~30 years ago. Here we demonstrate that non-covalent chalcogen bonding (Ch-bonding) is a distinct mode of interatomic connectivity for constructing functional materials by design. This is established by leveraging self-complementary assembly of 1,2,5-telluradiazole moieties to construct a honeycomb-type permanently porous Ch-bonded organic framework, assembled and stabilized solely through non-covalent Te...N contacts. Empirical and computational studies of electronic structure, structural healing and lattice dynamics highlight the pi-type electronic communication, controlled assembly and modulated lattice dynamics in Trip3Tez-I arising directly from the unique nature of the Te...N Ch-bonding that holds substantial implications for next generation crystalline semiconductors. In addition to introducing a distinct class of permanently porous frameworks, this work establishes Ch-bonding as a programmable molecular tool for constructing functional materials with distinct properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗