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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 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

A molecular ground electronic state with an occupied 5g spinor—The superheavy (E125)F molecule

Fully relativistic calculations, primarily at the 4-component coupled-cluster singles and doubles with perturbative triples [CCSD(T)] level of theory with the Dirac–Coulomb (DC) Hamiltonian, have been carried out for the superheavy (E125)F molecule using large Gaussian basis sets. The electronic ground state is determined to have an [Og]8s 2 5g 1 6f 3 configuration on E125 with an Ω = 6 ground state and an 8p electron largely donated to F. A Mulliken population analysis indicates that the ground state is mainly ionic with a partial charge of +0.79 on E125 and a single sigma bond involving the F 2p and E125 8p spinors. The occupied g spinor is not involved in the bonding. With the largest basis set used in this work, the (0 K) dissociation energy was calculated at the DC-CCSD(T) level of theory to be 7.02 eV. Analogous calculations were also carried out for the E125 atom, both the neutral and its cation. The lowest energy electron configuration of E125 + , [Og]$8s$$^{2}_{1/2}$$5g$$^{1}_{7/2}$$6f$$^{3}_{5/2}$ with a J = 6 ground state, was found to be similar to that in (E125)F, while the neutral E125 atom has an [Og]$8s$$^{2}_{1/2}$$5g$$^{1}_{7/2}$$6f$$^{2}_{5/2}$$7d$$^{1}_{3/2}$$8p$$^{1}_{1/2}$ ground state electron configuration with a J = 17/2 ground state. The ionization energy (IE) of E125 is reported for the first time and is calculated to be 4.70 eV at the DC-CCSD(T) level of theory. Non-relativistic calculations were also carried out on the E125 atom and the (E125)F molecule. Here, the non-relativistic ground state of the E125 atom was calculated to have a 5g 5 ground state with an IE of just 3.4 eV. The net effect of relativity on (E125)F is to stabilize its bonding.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2021

Impact of direct exchange coupling via the insulator on the magnetic tunnel junction based molecular spintronics devices with competing molecule induced inter-electrode coupling

The magnetic tunnel junction (MTJ) based molecular spintronics device (MTJMSD) approach is suitable for mass production. This approach provides solutions to fabrication difficulties related to reliably connecting molecular device elements to the ferromagnets (FMs). To producing MTJMSD, the molecular channels are bridged across the insulator of an MTJ testbed with exposed side edges. In an MTJMSD, two FMs are simultaneously connected by an insulator film and the molecular channels along the exposed sides. In our prior experimental studies, we observed that molecules could produce strong coupling between ferromagnets in the presence of the competing coupling via an insulator. In this paper, our Monte Carlo Simulation (MCS) was used to study the impact of coupling variation via insulator (a.k.a. Ji) on the magnetic properties of an MTJMSD. We studied the effect of Ji while varying the molecule induced antiferromagnetic exchange coupling. The ferromagnetic or antiferromagnetic nature and magnitude of Ji determined the resultant effect. Antiferromagnetic Ji enhanced the pre-existing antiferromagnetic molecular coupling effect. Ferromagnetic Ji competed with the opposite nature of antiferromagnetic molecular coupling. Our MCS may help to understand the impact of insulator thickness and defects on the molecular spintronics device performance and design process.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Stable metal anodes enabled by a labile organic molecule bonded to a reduced graphene oxide aerogel

Significance Rechargeable batteries based on metal anodes are highly desirable due to their high energy density. However, the electrochemical interface is generally not favorable for metal deposition, resulting in dendritic metal growth and an unstable solid–electrolyte interphase (SEI). We altered the interface using a labile organic molecule, benzenesulfonyl fluoride. This molecule was bonded to the surface of a reduced graphene oxide aerogel, which not only guides uniform metal deposition but also enables formation of a stable SEI layer. The lithium metal batteries showed stable cycling and excellent tolerance to low-temperature operation. Stable sodium and zinc anodes were also realized, demonstrating the versatility of this concept.

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

Identification of small-molecule protein–protein interaction inhibitors for NKG2D

NKG2D (natural-killer group 2, member D) is a homodimeric transmembrane receptor that plays an important role in NK, γδ + , and CD8 + T cell-mediated immune responses to environmental stressors such as viral or bacterial infections and oxidative stress. However, aberrant NKG2D signaling has also been associated with chronic inflammatory and autoimmune diseases, and as such NKG2D is thought to be an attractive target for immune intervention. Here, in this study, we describe a comprehensive small-molecule hit identification strategy and two distinct series of protein–protein interaction inhibitors of NKG2D. Although the hits are chemically distinct, they share a unique allosteric mechanism of disrupting ligand binding by accessing a cryptic pocket and causing the two monomers of the NKG2D dimer to open apart and twist relative to one another. Leveraging a suite of biochemical and cell-based assays coupled with structure-based drug design, we established tractable structure–activity relationships with one of the chemical series and successfully improved both the potency and physicochemical properties. Together, we demonstrate that it is possible, albeit challenging, to disrupt the interaction between NKG2D and multiple protein ligands with a single molecule through allosteric modulation of the NKG2D receptor dimer/ligand interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Combining MicroED and native mass spectrometry for structural discovery of enzyme–small molecule complexes

With the goal of accelerating the discovery of small molecule–protein complexes, we leverage fast, low-dose, event-based electron counting microcrystal electron diffraction (MicroED) data collection and native mass spectrometry. This approach, which we term electron diffraction with native mass spectrometry (ED-MS), allows assignment of protein target structures bound to ligands with data obtained from crystal slurries soaked with mixtures of known inhibitors and crude biosynthetic reactions. This extends to libraries of printed ligands dispensed directly onto TEM grids for later soaking with microcrystal slurries, and complexes with noncovalent ligands. ED-MS resolves structures of the natural product, epoxide-based cysteine protease inhibitor E-64, and its biosynthetic analogs bound to the model cysteine protease, papain. It further identifies papain binding to its preferred natural products, by showing that two analogs of E-64 outcompete others in binding to papain crystals, and by detecting papain bound to E-64 and an analog from crude biosynthetic reactions, without purification. ED-MS also resolves binding of the CTX-M-14 β-lactamase, a target of active drug development, to the non-β-lactam inhibitor, avibactam, alone or in a cocktail of unrelated compounds. These results illustrate the utility of ED-MS for natural product ligand discovery and for structure-based screening of small molecule binders to macromolecular targets, promising utility for drug discovery.

MicroED↗
DOE OSTI2022

Brighter, faster, stronger: ultrafast scattering of free molecules

Advances in FEL technologies have contributed remarkably to various scientific fields over the past decade, and ultrafast molecular dynamics is no exception. The ability to probe motions of the molecule via scattering provides uniquely direct structural information, which, when combined with traditional spectroscopic techniques of comparable temporal resolution, paints a holistic movie of the molecular dynamics. This review aims to provide an introduction to the ultrafast scattering of gas-phase molecules, and to identify the key results and technological breakthroughs that advance our acquaintance of ultrafast molecular dynamics, with a particular focus on the achievements in ultrafast molecular dynamics since the first generation of FEL facilities. We pre- sent a brief history of gas-phase ultrafast scattering and the fundamentals of electron- and x-ray scattering, highlighting the complementarity, differences, and bottlenecks of the two experimental scattering methods. Furthermore, we then consider key upgrades in XRS and UED experiments that facilitated the unprecedented spatiotemporal resolution that enabled many of the notable results in the field. Finally, we examine anticipated facility upgrades that address the demand for experimental versatility and enable further developments and exploration.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

High intensity x-ray interaction with a model bio-molecule system: double-core-hole states and fragmentation of formamide

Formamide, a simple model bio-molecule (HCONH 2 ), is irradiated with high intensity, ultrashort pulses from an x-ray free electron laser. Ionic fragments resulting from photoionization and subsequent decay processes are recorded, as well as the electronic signature of the different inner shell ionization events that can take place during the x-ray pulses. Additionally, the formation of double-core-hole states, where a second inner shell electron is removed before the first core hole has been refilled is observed in the electron spectra, recorded at all three sites (C, N, O) of the molecule. The individual ionization potentials are compared with results of ab initio calculations at different level of theory. Based on our results, future opportunities for advanced studies of inner-shell-induced electronic and nuclear dynamics are explored.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

The missing base molecules in atmospheric acid–base nucleation

Abstract Transformation of low-volatility gaseous precursors to new particles affects aerosol number concentration, cloud formation and hence the climate. The clustering of acid and base molecules is a major mechanism driving fast nucleation and initial growth of new particles in the atmosphere. However, the acid–base cluster composition, measured using state-of-the-art mass spectrometers, cannot explain the measured high formation rate of new particles. Here we present strong evidence for the existence of base molecules such as amines in the smallest atmospheric sulfuric acid clusters prior to their detection by mass spectrometers. We demonstrate that forming (H2SO4)1(amine)1 is the rate-limiting step in atmospheric H2SO4-amine nucleation and the uptake of (H2SO4)1(amine)1 is a major pathway for the initial growth of H2SO4 clusters. The proposed mechanism is very consistent with measured new particle formation in urban Beijing, in which dimethylamine is the key base for H2SO4 nucleation while other bases such as ammonia may contribute to the growth of larger clusters. Our findings further underline the fact that strong amines, even at low concentrations and when undetected in the smallest clusters, can be crucial to particle formation in the planetary boundary layer.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A small molecule antagonizes jasmonic acid perception and auxin responses in vascular and nonvascular plants

The phytohormone jasmonoyl-L-isoleucine (JA-Ile) regulates many stress responses and developmental processes in plants. A co-receptor complex formed by the F-box protein Coronatine Insensitive 1 (COI1) and a Jasmonate (JA) ZIM-domain (JAZ) repressor perceives the hormone. JA-Ile antagonists are invaluable tools for exploring the role of JA-Ile in specific tissues and developmental stages, and for identifying regulatory processes of the signaling pathway. Using two complementary chemical screens, we identified three compounds that exhibit a robust inhibitory effect on both the hormone-mediated COI–JAZ interaction and degradation of JAZ1 and JAZ9 in vivo. One molecule, J4, also restrains specific JA-induced physiological responses in different angiosperm plants, including JA-mediated gene expression, growth inhibition, chlorophyll degradation, and anthocyanin accumulation. Interaction experiments with purified proteins indicate that J4 directly interferes with the formation of the Arabidopsis (Arabidopsis thaliana) COI1–JAZ complex otherwise induced by JA. The antagonistic effect of J4 on COI1–JAZ also occurs in the liverwort Marchantia polymorpha, suggesting the mode of action is conserved in land plants. Besides JA signaling, J4 works as an antagonist of the closely related auxin signaling pathway, preventing Transport Inhibitor Response1/Aux–indole-3-acetic acid interaction and auxin responses in planta, including hormone-mediated degradation of an auxin repressor, gene expression, and gravitropic response. However, J4 does not affect other hormonal pathways. Altogether, our results show that this dual antagonist competes with JA-Ile and auxin, preventing the formation of phylogenetically related receptor complexes. J4 may be a useful tool to dissect both the JA-Ile and auxin pathways in particular tissues and developmental stages since it reversibly inhibits these pathways. One-sentence summary: A chemical screen identified a molecule that antagonizes jasmonate perception by directly interfering with receptor complex formation in phylogenetically distant vascular and nonvascular plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Attosecond X-Ray Core-Level Chronoscopy of Aromatic Molecules

Attosecond photoemission or photoionization delays are a unique probe of the structure and the electronic dynamics of matter. However, the spectral congestion of valence photoelectron spectra sets fundamental limits to the complexity of systems that can be studied, and the delocalization of valence electron wave functions blurs the spatial origin of the photoelectron wave packet. Using attosecond x-ray pulses from LCLS, we demonstrate the key advantages of measuring core-level delays: The photoelectron spectra remain atomlike, the measurements become element specific, and the observed scattering dynamics originate from a pointlike source when multicenter interference effects are negligible. We exploit these unique features to reveal the effects of changing functional groups (C-H vs N) and symmetry on attosecond scattering dynamics by measuring and calculating the photoionization delays between N−1⁢𝑠 and C−1⁢𝑠 core shells of a series of aromatic azabenzene molecules. Remarkably, the delays increase with the number of nitrogen atoms in the molecule and reveal multiple resonances. We identify two previously unknown mechanisms regulating the associated attosecond dynamics, namely the enhanced confinement of the trapped wave function with the replacement of C-H groups by N atoms and the decrease of the coupling strength among the photoemitted partial waves with increasing symmetry. This study demonstrates the unique opportunities opened by measurements of core-level photoionization delays for unraveling attosecond electron dynamics in complex matter.

Ji, Jia-Bao [Eidgenoessische Technische Hochschule↗
DOE OSTI2021

Orbital-resolved calculations of two-center interferences in linear triatomic molecules

In this report we perform ab initio calculations of high-harmonic spectroscopy (HHS) of two-center interference phenomena in oriented carbon-dichalcogen molecules, using time-dependent density functional theory (TDDFT). We show that by resolving the harmonic response into contributions from individual Kohn-Sham orbitals, we can extract target-specific characteristics for both the spectral amplitude and phase. We also discuss that this extraction is predicated on a careful analysis and normalization of the harmonic spectrum. Finally, we present field-free scattering calculations that mimic the recollision step in high-order-harmonic generation and allow the calculation of recombination dipole matrix elements without explicitly calculating the scattering states of a molecule. We show that the orbital-resolved TDDFT HHS results and results based on our field-free scattering calculations are in very good agreement with each other.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Genetic-algorithm retrieval of the molecular alignment distribution with high-order harmonics generated from transiently aligned CO 2 molecules

Using genetic algorithm, we propose a method to retrieve the alignment distribution of transiently aligned CO 2 molecules from the high-order harmonic generation (HHG) spectra. The retrieval method is based on the quantitative rescattering (QRS) model where averaged photorecombination transition dipole can be factored out from the parallel (or perpendicular) harmonic spectra after the propagation of the harmonic fields in the gas medium. We examine how the retrieved alignment distributions are affected by uncertainty in alignment dependent ionization probability and on multiple orbital contribution to the HHG. We further confirm that alignment distribution is more accurately retrieved by using the minima in the HHG spectra driven by a long-wavelength laser. In addition, we show that earlier experimental data on the ratios between the perpendicular and the parallel HHG components of aligned CO 2 molecules are in better agreement with the QRS model if the macroscopic propagation and multiple orbital interference are included in the theoretical calculation.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Density-matrix approach for sequential dissociative double ionization of molecules

Intense femtosecond infrared (IR) laser pulses have been used in recent years to study the breakup dynamics of molecules. However, observables such as kinetic energy release and branching ratios of molecular fragments are often difficult to predict by theory, making information of the molecular dynamics difficult to retrieve. In this work, we develop a simple model for sequential double ionization of molecules based on a density-matrix approach. The model describes tunneling ionization of the neutral and the ion as well as laser couplings between the ionic states simultaneously. Population of different doubly charged states can be obtained at a low computational cost. Furthermore, we applied our model to N 2 and obtained a good agreement on the kinetic energy release spectrum with a previous experiment. This theoretical development could open up the opportunities to use intense short IR laser pulses with coincidence measurement to probe molecular dynamics.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Coherence from multiorbital tunneling ionization of molecules

We present a simple and general coherence model for multiorbital tunnel ionization of molecules, which we incorporate into our previously developed density-matrix approach for sequential double ionization. Here, the influence of this coherence is investigated through simulations of single ionization and sequential double ionization of N 2 and O 2 using few-cycle near-infrared laser pulses. In the case of single ionization, our results reveal the crucial role played by this coherence in generating population inversion in N 2 + , suggesting a potential mechanism for air lasing. Regarding sequential double ionization, we observe only minor changes in the kinetic energy release spectra when the coherence is included, while noticeable differences in the angle-dependent dication yield for both N 2 and O 2 are found. Based on these findings, we recommend the inclusion of multiorbital tunnel ionization coherence in models for single ionization of general molecules, while suggesting that it can be safely neglected in the case of sequential double ionization.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Quantum tracking control of the orientation of symmetric-top molecules

The goal of quantum tracking control is to identify shaped fields to steer observable expectation values along designated time-dependent tracks. The fields are determined via an iteration-free procedure, which is based on inverting the underlying dynamical equations governing the controlled observables. In this paper, we generalize the ideas in [Phys. Rev. A 98, 043429 (2018)] to the task of orienting symmetric top molecules in three dimensions. To this end, we derive equations for the control fields capable of directly tracking the expected value of the three-dimensional dipole orientation vector along a desired path in time. In conclusion, we show this framework can be utilized for tracking the orientation of linear molecules as well, and present numerical illustrations of these principles for symmetric-top tracking control problems.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Efficient graph representation framework for chemical molecule similarity tasks

Graph data has emerged in numerous scientific domains and machine learning techniques have been widely used for analysis and learning of diverse data for prediction and decision. Machine learning techniques can readily address complex problems by leveraging their structural information. But graphs cannot be directly used for existing machine learning algorithms unless encoded as vectors. The problem of efficient representation of graphs is a substantial challenge in graph machine learning. In this paper, we propose a novel two-stage framework for the representation of chemical molecule graphs based on the strengths of Graph Isomorphism Networks (GINs) and Siamese autoencoders. In the first stage, the GIN model is constructed and trained using the structural information of chemical molecule graphs. Node attributes, edge attributes, and edge indices are used as input data, while graph attributes are used as labels. The GIN model effectively captures the structural characteristics of graphs and can accurately predict graph attributes, i.e., molecular properties. It also generates Graph Embeddings, represented as vectors that encode the structural information of graphs. In the second stage, Graph Embedding vectors are further optimized for downstream similarity tasks while preserving the graph structural information. The Siamese autoencoder is constructed and trained, which reduces the dimensionality of the Graph Embedding vectors, while maximizing the preservation of structural information in the original high-dimensional vectors. The resulting low-dimensional Graph Embeddings can be effectively utilized for tasks such as approximate nearest neighbor search. The experimental results demonstrate the effectiveness of our proposed framework in accurately predicting graph similarity.

Ma, Jiaji↗
DOE OSTI2021

FL-DISCO: Federated Generative Adversarial Network for Graph-based Molecule Drug Discovery: Special Session Paper

The outbreak of the global COVID-19 pandemic emphasizes the importance of collaborative drug discovery for high effectiveness; however, due to the stringent data regulation, data privacy becomes an imminent issue needing to be addressed to enable collaborative drug discovery. In addition to the data privacy issue, the efficiency of drug discovery is another key objective since infectious diseases spread exponentially and effectively conducting drug discovery could save lives. Advanced Artificial Intelligence (AI) techniques are promising to solve these problems: (1) Federated Learning (FL) is born to keep data privacy while learning data from distributed clients; (2) graph neural network (GNN) can extract structural properties of molecules whose underlying architecture is the connected atoms; and (3) generative adversarial network (GAN) can generate novel molecules while retaining the properties learned from the training data. In this work, we make the first attempt to build a holistic collaborative and privacy-preserving FL framework, namely FL- DISCO, which integrates GAN and GNN to generate molecular graphs. Experimental results demonstrate the effectiveness of FL- DISCO on: (1) IID data for ESOL and QM9, where FL-DISCO can generate highly novel compounds with high drug-likeliness, uniqueness and LogP scores compared to the baseline; (2) non- IID data for ESOL and QM9, where FL-DISCO generates 100% novel compounds with high validity and LogP scores compared to the baseline. We also demonstrate how different fractions of clients, generator and discriminator architectures affect our evaluation scores.

Manu, Daniel↗
DOE OSTI2021

X-ray spectroscopic identification of strain and structure-based resonances in a series of saturated carbon-cage molecules: Adamantane, twistane, octahedrane, and cubane

Novel nanocarbons such as fullerenes, nanotubes, graphene, and nanodiamond reside at the cutting edge of nanoscience and technology. Along with chemical functionalization, geometric constraints (such as extreme curvature in nanotubes or defects within or at the surfaces of diamond nanoparticles) significantly alter the electronic states of the nanocarbon material. Understanding the effects of steric strain on the electronic structure is critical to developing nanoelectronic applications based on these materials. This paper presents a fundamental study of how strain affects the electronic structure in a benchmark series of some fundamental saturated carbon cage compounds. Adamantane, C10H16, the smallest diamondoid and arguably the smallest nanodiamond crystallite, has carbon atoms essentially commensurate with diamond lattice positions and possesses by far the least molecular strain of this series. Twistane also is a C10H16 isomer but the fixed cyclohexane twist conformation of the central ring introduces additional strain into the cage. Octahedrane [(CH)12] and cubane [(CH)8] are considerably more strained, culminating in cubane where carbon–carbon bonds lie either parallel or orthogonal to one another. Using gas-phase near-edge x-ray absorption fine structure spectroscopy to probe the unoccupied electronic states, we observe two major progressions across this series. First, a broad C–C σ* resonance in the absorption splits into two more narrow and intense resonances with increasing strain. Second, the first manifold of states previously associated with tertiary C–H σ* in the diamondoid series appears to broaden and shift to lower energy. This feature is more than twice as intense in cubane than in octahedrane, even though these two molecules have only tertiary carbons, with the chemical formula (CH)x. The spectral differences are entirely due to the shape of the molecules; in particular, in cubane, the features arise from a high degree of p-p interaction between parallel C–C bonds. In contrast to the conventional wisdom that near-edge x-ray absorption is primarily an atomically localized spectroscopy, molecular shape and associated strain lead to the dominant features in spectra acquired from this fundamental series of carbon cage structures.

36 MATERIALS SCIENCE↗