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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Antiviral discovery using sparse datasets by integrating experiments, molecular simulations, and machine learning

Computational methods have demonstrated success in identifying virucidal agents, effectively contributing to the discovery of novel virucidal molecules. In this study, we developed a machine learning (ML) model, trained on a small dataset, to predict inhibitors of human enterovirus 71 (EV71), a pathological agent that causes severe disease in children and immunocompromised adults. Despite the dataset’s limitation, comprising of only 36 compounds tested, our ML framework demonstrated significant predictive capability. Notably, experimental validation revealed that five out of the eight compounds predicted by our model from the Chinese cosmetic material list exhibited virucidal activity. The inhibitor effects displayed by the main active compounds were further confirmed by molecular dynamics simulation. This underscores the potential of our AI-driven approach to bypass data constraints in identifying active molecules against viral pathogens.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Atomic-Scale Structural Mapping of Active Sites in Monolayer PGM-Free Catalysts by Low-Voltage 4D-STEM

Two-dimensional (2D) materials have attracted a large amount of attention in both basic and applied fields, and scanning transmission electron microscopy (STEM) is often uniquely well-suited for characterizing the atomic-scale structure of these materials [1-4]. As a result, STEM is poised to significantly impact progress on platinum group metal (PGM)-free catalysts, which are currently under intense development to enable low-cost, commercially viable hydrogen fuel cells [5]. While recent advancements have resulted in fuel cell performance comparable to Pt catalysts by some measures [6], cell durability remains a significant challenge, limiting practical applications [7]. Catalytically active sites in PGM-free materials are proposed to be FeN4 complexes embedded in a graphene lattice (Fig. 1b) within layered or other larger materials, but this is still under debate largely due to the range of potential actives sites predicted by computational methods and lack of methods for directly validating these models [5]. Fundamental insights into the atomic structure and resulting degradation pathways of proposed active sites are therefore needed to fully understand and control cell performance and durability [6].2D materials typically make ideal samples for STEM, but those within PGM-free catalysts present additional challenges since these materials are often defect-rich, with a high density of edges, dopant atoms, etc., which significantly increase susceptibility to beam damage at standard operating voltages. This makes analysis of potential FeN4 active sites particularly challenging, since a large proportion of Fe exists at edge sites where beam-induced atomic displacements can prohibit high-resolution structural characterization [6]. Conventional dark-field imaging compounds this problem by producing less signal for a given dose and being less sensitive to light elements than dose-efficient phase contrast imaging techniques such as those enabled by four-dimensional (4D)-STEM [8-10] (Fig. 1a). Consequently, active site structural analysis is often left to methods such as low-resolution imaging combined with quantum chemical calculations [6], which hinders accurate determination of reaction and degradation mechanisms.Here, we demonstrate direct atomic-scale structural mapping of FeN4 sites by performing low-voltage 4D-STEM on a model PGM-free catalyst system with many exposed monolayer regions. To accomplish this, we pair a 30 keV aberration-corrected probe with a fast pixelated detector that has optimal performance at low beam voltages [11]. This enables us to simultaneously image light and heavy elements with high signal-to-noise by center-of-mass analysis (Fig. 1c) while minimizing beam-induced atomic displacements at sensitive sites. The monolayer nature of these materials additionally allows for experimental validation by direct comparison with multislice simulations [12] of model structures (Fig. 1d-e). This work demonstrates how low-voltage 4D-STEM will provide new insights into the atomic-scale structure and degradation mechanisms of active sites in PGM-free catalysts, facilitating the development of low-cost hydrogen fuel cells and other energy conversion technologies in the future [13].

Zachman, Michael↗
DOE OSTI2021

py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis

Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Characterization of the In Vivo Deuteration of Native Phospholipids by Mass Spectrometry Yields Guidelines for Their Regiospecific Customization

Customization of deuterated biomolecules is vital for many advanced biological experiments including neutron scattering. However, because it is challenging to control the proportion and regiospecificity of deuterium incorporation in live systems, often only two or three synthetic lipids are mixed together to form simplistic model membranes. This limits the applicability and biological accuracy of the results generated with these synthetic membranes. Despite some limited prior examination of deuterating Escherichia coli lipids in vivo, this approach has not been widely implemented. In this report an extensive mass spectrometry-based profiling of E. coli phospholipid deuteration states with several different growth media was performed, and a computational method to describe deuterium distributions with a one-number summary is introduced. The deuteration states of 36 lipid species were quantitatively profiled in 15 different growth conditions, and tandem mass spectrometry was used to reveal deuterium localization. Regressions were employed to enable the prediction of lipid deuteration for untested conditions. Small-angle neutron scattering was performed on select deuterated lipid samples, which validated the deuteration states calculated from the mass spectral data. Based on these experiments, guidelines for the design of specifically deuterated phospholipids are described. This unlocks even greater capabilities from neutron-based techniques, enabling experiments that were formerly impossible.

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

Increasing the Scale of the Mass Spectrometry Query Language Compendium with Explainable AI

A significant bottleneck in metabolomics data interpretation is the effective use of domain knowledge to assign structural information based on fragmentation patterns. The mass spectrometry query language (MassQL) aims to make this process accessible and applicable across multiple analysis platforms. While advanced computational methods are capable of predicting compound structures from fragmentation data, AI/ML approaches often rely on complex, opaque criteria that are difficult to interpret or modify. As a result, their predictive patterns cannot be readily translated into human-readable rules, such as those used in MassQL. Here, in this study, we introduce ChemEcho, a machine learning embedding method that converts tandem mass spectrometry data into sparse feature vectors containing peak and neutral mass subformulae to enhance explainable AI/ML-based methods. An advantage of this approach is that decision trees trained using these feature vectors can be directly translated to MassQL. Using a battery of decision trees trained using ChemEcho embeddings to predict molecular attributes, we generated over 1500 MassQL queries for 765 molecular features and evaluated their precision and recall. From these queries, the 50 highest-performing queries were integrated into the MassQL compendium. This set of generated MassQL queries included environmentally and biologically relevant classes such as PFAS and molecules containing phosphate or sulfate substructures. To illustrate the impact these queries would have on a typical metabolomics experiment, these MassQL queries were applied to a public metabolomics data set─resulting in a marked increase in the structural information derived from tandem mass spectra. Access and reuse of these queries is expected to enhance structural annotation in untargeted experiments, leading to more specific claims and advancing many applications in metabolomics.

Harwood, Thomas V. [USDOE Joint Genome Institute (↗
DOE OSTI2020

Dynamics of Hydroxyl Anions Promotes Lithium Ion Conduction in Antiperovskite Li 2 OHCl

Li 2 OHCl is an exemplar of the antiperovskite family of ionic conductors, for which high ionic conductivities have been reported, but in which the atomic-level mechanism of ion migration is unclear. The stable phase is both crystallographically defective and disordered, having similar to 1/3 of the Li sites vacant, while the presence of the OH(- )anion introduces the possibility of rotational disorder that may be coupled to cation migration. In this work, complementary experimental and computational methods are applied to understand the relationship between the crystal chemistry and ionic conductivity in Li 2 OHCl , which undergoes an orthorhombic to cubic phase transition near 311 K (approximate to 38 degrees C) and coincides with the more than a factor of 10 change in ionic conductivity (from 1.2 x 10 -5 mS/cm at 37 degrees C to 1.4 x 10 -3 mS/cm at 39 degrees C). X ray and neutron experiments conducted over the temperature range 20-200 degrees C, including diffraction, quasi-elastic neutron scattering (QENS), the maximum entropy method (MEM) analysis, and ab initio molecular dynamics (AIMD) simulations, together show conclusively that the high lithium ion conductivity of cubic Li2OHCl is correlated to "paddlewheel" rotation of the dynamic OH - anion. The present results suggest that in antiperovskites and derivative structures a high cation vacancy concentration combined with the presence of disordered molecular anions can lead to high cation mobility.

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

In Silico Guidance for In Vitro Androgen and Glucocorticoid Receptor ToxCast Assays

Molecular initiating events (MIEs) are key events in adverse outcome pathways (AOPs) that link molecular chemistry to target biology. As they are based in chemistry, these interactions are excellent targets for computational chemistry approaches to in silico modelling. In this work, we aim to link ligand chemical structure to MIEs for androgen receptor (AR) and glucocorticoid receptor (GR) binding using ToxCast data. This has been done using an automated computational algorithm to perform maximal common substructure searches on chemical binders for each target from the ToxCast dataset. The models developed show a high level of accuracy, correctly assigning 87.20% of AR binders and 96.81% of GR binders in a 25% test set using holdout cross-validation. The 2D structural alerts developed can be used as in silico models to predict these MIEs, and as guidance for in vitro ToxCast assays to confirm hits. These models can target such experimental work, reducing the number of assays to be performed to gain required toxicological insight. Development of these models has also allowed some structural alerts to be identified as predictors for agonist or antagonist behavior at the receptor target. This work represents a first step in using computational methods to guide and target experimental approaches.

Allen, Timothy H.↗
DOE OSTI2020

Perturbation of 1 J C,F Coupling in Carbon–Fluorine Bonds on Coordination to Lewis Acids: A Structural, Spectroscopic, and Computational Study

A lithiated m-terphenyl ligand bearing fluorine atoms at the ortho positions of the flanking aryl rings was synthesized and characterized using single crystal X-ray diffraction, variable-temperature multinuclear NMR spectroscopy, and computational methods. Here, changes in 1 J C,F on coordination to lithium as a spectroscopic observable parametrizing the strength of the C–F···Li interaction are described, and a general, qualitative relationship between C–F bond lengths, Δ 1 J C,F values, and the extent of C–F bond activation as a result of Lewis acid coordination is proposed.

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

Four-Coordinate Fe N 2 and Imido Complexes Supported by a Hemilabile NNC Heteroscorpionate Ligand

Inspired by mechanistic proposals for N 2 reduction at the nitrogenase FeMo cofactor, we report herein a new, strongly σ-donating heteroscorpionate ligand featuring two weak-field pyrazoles and an alkyl donor. This ligand supports four-coordinate Fe(I)-N 2 , Fe(II)-Cl, and Fe(III)-imido complexes, which we have characterized using a variety of spectroscopic and computational methods. Structural and quantum mechanical analysis reveal the nature of the Fe–C bonds to be essentially invariant between the complexes, with conversion between the (formally) low-valent Fe-N 2 and high-valent Fe-imido complexes mediated by pyrazole hemilability. This presents a useful strategy for substrate reduction at such low-coordinate centers and suggests a mechanism by which FeMoco might accommodate the binding of both π-acidic and π-basic nitrogenous substrates.

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

General Protocol for the Accurate Prediction of Molecular 13 C/ 1 H NMR Chemical Shifts via Machine Learning Augmented DFT

An accurate prediction of NMR chemical shifts at affordable computational cost is very important for different types of structural assignments in experimental studies. Density functional theory (DFT) and gauge-including atomic orbital (GIAO) are two of the most popular computational methods for NMR calculation, yet they often fail to resolve ambiguities in structural assignments. In this work, we present a new method that uses machine learning (ML) techniques (DFT + ML) that significantly increases the accuracy of 13 C/ 1 H NMR chemical shift prediction for a variety of organic molecules. The input of the generalizable DFT + ML model contains two critical parts: one is a vector providing insights into chemical environments, which can be evaluated without knowing the exact geometry of the molecule; the other one is the DFT-calculated isotropic shielding constant. The DFT + ML model was trained with a data set containing 476 13 C and 270 1 H experimental chemical shifts. For the DFT methods used here, the root mean square deviations (RMSDs) for the errors between predicted and experimental 13 C/ 1 H chemical shifts can be as small as 2.10/0.18 ppm, which is much lower than those from simple DFT (5.54/0.25 ppm), or DFT + linear regression (LR) (4.77/0.23 ppm) approaches. It also has a smaller maximum absolute error than two previously proposed NMR-predicting ML models. The robustness of the DFT + ML model is tested on two classes of organic molecules (TIC10 and hyacinthacines), where the correct isomers were unambiguously assigned to the experimental ones. Overall, the DFT + ML model shows promise for structural assignments in a variety of systems, including stereoisomers, that are often challenging to determine experimentally.

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

Systematic Improvement of Quantum Monte Carlo Calculations in Transition Metal Oxides: sCI-Driven Wavefunction Optimization for Reliable Band Gap Prediction

Accurate determination of the electronic properties of correlated oxides remains a significant challenge for computational theory. Traditional Hubbard-corrected density functional theory (DFT+U) frequently encounters limitations in precisely capturing electron correlation, particularly in predicting band gaps. We introduce a systematic methodology to enhance the accuracy of diffusion Monte Carlo (DMC) simulations for both ground and excited states, focusing on LiCoO 2 as a case study. By employing a selected configuration interaction (sCI) approach, we demonstrate the capability to optimize wavefunctions beyond the constraints of single-reference DFT+U trial wavefunctions. Here, we show that the sCI framework enables accurate prediction of band gaps in LiCoO 2 , closely aligning with experimental values and substantially improving traditional computational methods. The study uncovers a nuanced mixed state of t 2g and e g orbitals at the band edges that is not captured by conventional single-reference methods, further elucidating the limitations of PBE+U in describing d-d excitations. Our findings advocate for the adoption of beyond-DFT methodologies, such as sCI, to capture the essential physics of excited-state wavefunctions in strongly correlated materials. The improved accuracy in band gap predictions and the ability to generate more reliable trial wavefunctions for DMC calculations underscore the potential of this approach for broader applications in the study of correlated oxides. This work not only provides a pathway for more accurate simulations of electronic structures in complex materials but also suggests a framework for future investigations of the excited states of other challenging systems.

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

Experimental and Theoretical Study of Oxolan-3-one Thermal Decomposition

The thermal decomposition of oxolan-3-one, a common component of the bio-oil formed during biomass pyrolysis, has been studied using ab initio calculations and experiments employing pulsed gas-phase pyrolysis with matrix isolation FTIR product detection. Four pathways for unimolecular decomposition were predicted using computational methods. The dominant reaction channel led to carbon monoxide, formaldehyde, and ethylene, all of which were observed experimentally. Here, the other channels led to an assortment of products including ketene, water, propyne, and acetylene, which were all confirmed in the matrix-isolation FTIR spectra. There is also evidence for the production of substituted ketenes in pyrolysis, most likely hydroxyketene and methylketene.

09 BIOMASS FUELS↗
DOE OSTI2020

Realistic Ion Dynamics through Charge Renormalization in Nonaqueous Electrolytes

While many practically important electrolytes contain lithium ions, interactions of these ions are particularly difficult to probe experimentally because of their small X-ray and neutron scattering cross sections and large neutron absorption cross sections. Molecular dynamics (MD) is a powerful tool for understanding the properties of nonaqueous electrolyte solutions from the atomic level, but the accuracy of this computational method crucially depends on the physics built into the classical force field. In this study, we demonstrate that several force fields for lithium bistriflimide (LiTFSI) in acetonitrile yield a solution structure that is consistent with the neutron scattering experiments, yet these models produce dramatically different ion dynamics in solution. Such glaring discrepancies indicate that inadequate representation of long-range interactions leads to excessive ionic association and ion-pair clustering. We show that reasonable agreement with the experimental observations can be achieved by renormalization of the ion charges using a “titration” method suggested herewith. This simple modification produces realistic concentration dependencies for ionic diffusion and conductivity in <2 M solutions, without loss in quality for simulation of the structure.

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

Concentration-Dependent Solvation Structure and Dynamics of Aqueous Sulfuric Acid Using Multinuclear NMR and DFT

Sulfuric acid is a ubiquitous compound for industrial processes and aqueous sulfate solutions also play a critical role in electrolytes for many prominent battery chemistries. While the thermodynamic literature for it is quite well-developed, comprehensive studies of the solvation structure, and particularly molecular-scale dynamical and transport properties, are less available. This study applies a multinuclear NMR approach to the elucidation of the solvation structure and dynamics over a wide temperature (-10 – 50?C) and concentration (0 – 18 M) range, combining 17O shift, linewidth, and T1 relaxation measurements, 33S shift and linewidth measurements, and 1H PFG-NMR measurements of the proton self-diffusivity. In conjunction, these results indicate a crossover between two regimes of solvation structure and dynamics, occurring above the concentration associated with the deep eutectic point (~ 4.5 M), with the high-concentration regime dominated by strong water-sulfate correlation. This description was borne out in detail by the activation energy trends with increasing concentration derived from the relaxation of both the H2O/H3O+ and H2SO4/HSO4-/SO42- 17O resonances and the 1H self-diffusivity. However, the 17O chemical shift difference between the H2O/H3O+ and H2SO4/HSO4-/SO42- resonances across the entire temperature range is nevertheless strikingly linear. A computational approach coupling MD simulations and DFT NMR shift calculations to reproduce this trend is presented, which will be the subject of further development. This combination of multinuclear, dynamical NMR and computational methods, and the results furnished by this study, will provide a platform for future studies on battery electrolytes where aqueous sulfate chemistry plays a central role in the solution structure.

Bazak, Jonathan D.↗
DOE OSTI2022

Structural and Electronic Effect Driven Distortions in Visible Light Absorbing Polar Materials A Ta 2 V 2 O 11 ( A = Sr, Pb)

Complex vanadates of tantalum(V), such as ATa 2 V 2 O 11 (A = Sr, Pb), are rare and underrated materials, which have potential application domains that could be substantially expanded, mitigating the existing controversy on their atomic and electronic organization. Herein, we present a thorough structural examination combining synchrotron powder X-ray diffraction-aided distortion mode analysis with computational methods to study hettotypes of SrTa 2 V 2 O 11 (STVO) and PbTa 2 V 2 O 11 (PTVO). Being distinct from the perovskite family due to the presence of [VO 4 ] groups, both compounds are polar dielectric materials with certain similarities to SBT and PBT Aurivillius phases. Applying the model of anions of metallic matrices to the analysis of electron localization functions calculated on top of as-established equilibrium structures helps retrace the effects in the Sr and Pb surroundings on the respective crystal packings of STVO and PTVO.

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

Impact of Disorder and Defects on Bond Energies in Highly Fluorinated Graphene

Fluorinated graphite materials are of interest for an assortment of applications and can be synthesized under a variety of synthetic conditions from many different types of carbon. Due to such variations, structural disorders in the form of defects and polymorphism are often present. Here, we investigate the impact of local structural variations on the C–F bond dissociation energies (BDEs) in carbon-based fluoride materials using density functional theory (DFT) computational methods. Employing fluorographene (FG) cluster models, we determine the impact of different C–F bonding configurations in the core of each platelet on the equilibrium BDEs for each C–F bond. The introduction of structural disorder decreases the first C–F BDE by approximately 1 eV compared to the canonical arrangement of axial C–F bonds ordered as in a network of cyclohexane “chairs”. Variability of calculated BDEs among the different polymorphs decreases upon subsequent F removal. Common structural tendencies of the adiabatic defluorination pathways for each polymorph are identified. In conclusion, our analysis suggests that at F/C ratios near 1.0, disorder in the local structure can play a significant role in the energetics of the initial carbon fluoride defluorination and that the influence of this configurational disorder diminishes with decreasing F/C ratios.

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

Benchmarking DFT Accuracy in Predicting O 1s Binding Energies on Metals

X-ray photoelectron spectroscopy (XPS) is a powerful tool for probing the electronic structure and composition of materials, particularly metals and metal oxides of relevance to solar cells and catalysis. Density functional theory (DFT) is often used to support XPS peak assignments, but its reliability for predicting oxygen species is not well established. Here, we compile a large data set of experimental oxygen binding energies and evaluate corresponding DFT predictions. We find that as the binding energies of metal-bound atomic oxygen species increase, especially above ≈530 eV, there is a general decrease in the accuracy of DFTpredicted values. Thus, high-binding-energy atomic oxygen species, such as those proposed as active for selective Ag-catalyzed epoxidation, are less well represented. The chemical nature of the oxygen species also influences accuracy, with molecularly bound species more reliably captured across the entire range of energies. These findings illustrate the limitations of DFT for interpreting XPS spectra and provide a benchmark for improving computational methods.

Adsorption↗
DOE OSTI2024

Chloride, Alkoxide, or Silicon: The Bridging Ligand Dictates the Spin State in Dicobalt Expanded Pincer Complexes

We report the synthesis and characterization of a series of high- and low-spin dicobalt complexes of the tBu PNNP expanded pincer ligand. Reacting this dinucleating ligand in its neutral form with two equiv of CoCl 2 (tetrahydrofuran) 1.5 yields a high-spin dicobalt complex featuring one Co inside and one Co outside of the dinucleating pocket. Performing the same reaction in the presence of two equivalents of KOtBu provides access to a high-spin dicobalt complex wherein both Co centers are bound within the PNNP pocket, and this complex also features a bridging OtBu ligand. Reacting either of the high-spin complexes with excess diethyl silane affords a low-spin dicobalt complex containing two unusual bridging Si-based ligands. These complexes were investigated using NMR spectroscopy, XAS, single crystal X-ray structure determination, and computational methods, showing that the Si-based ligands are best described as base-stabilized silylenes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗