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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Quasiclassical sampling and Wigner sampling of initial vibrational coordinates and momenta for polyatomic molecules in Monte Carlo molecular dynamics simulations

In a quasiclassical trajectory simulation, the vibrational modes are initialised with quantised vibrational energies, but vibrational phases are sampled by Monte Carlo. This requires an algorithm to assign coordinates and momenta to the various atoms. In this work, we present two methods for implementing this for nonrotating polyatomic molecules, namely, fixed-energy vibrational-state-selected initial conditions and thermal initial conditions. We also present a method for initiating classical trajectories with a ground-state Wigner distribution. These vibrational treatments are sufficient to initialise trajectories for unimolecular processes, and we also show how they can be applied to simulate bimolecular collision processes. The treatments of unimolecular and bimolecular collision processes are available in two Python codes called wigner_state_selected.py and bimolecular_collision.py, respectively, which will generate initial condition files that are recognisable by the SHARC and SHARC-MN computer programs for dynamics calculations. Both codes are available as standalone programs, as well as being included in SHARC-MN, and they will be included in future versions of SHARC. Here, the methods implemented in these codes are mostly also available in the ANT computer program, and those that are not available in ANT will be incorporated in future versions of ANT.

Wigner distribution↗
DOE OSTI2024

Quantitative x-ray scattering of free molecules

Advances in x-ray free electron lasers have made ultrafast scattering a powerful method for investigating molecular reaction kinetics and dynamics. Accurate measurement of the ground-state, static scattering signals of the reacting molecules is pivotal for these pump-probe x-ray scattering experiments as they are the cornerstone for interpreting the observed structural dynamics. Here, this article presents a data calibration procedure, designed for gas-phase x-ray scattering experiments conducted at the Linac Coherent Light Source x-ray Free-Electron Laser at SLAC National Accelerator Laboratory, that makes it possible to derive a quantitative dependence of the scattering signal on the scattering vector. A self-calibration algorithm that optimizes the detector position without reference to a computed pattern is introduced. Angle-of-scattering corrections that account for several small experimental non-idealities are reported. Their implementation leads to near quantitative agreement with theoretical scattering patterns calculated with ab-initio methods as illustrated for two x-ray photon energies and several molecular test systems.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

D–MOPH–25: diverse MOF–molecule pairs for Henry’s constants prediction

Computational methods like grand-canonical Monte Carlo simulations and machine learning (ML) have accelerated metal–organic frameworks (MOF) exploration but are typically limited to a narrow range of adsorbates due to data availability and force field constraints. In this study, we introduce a dataset of diverse MOF–molecule pairs for Henry’s constant prediction, D–MOPH–25, which systematically explores a diverse chemical space by combining 113 molecular adsorbates with over 5000 MOF structures through an active learning process. D–MOPH–25 constitutes the most diverse adsorbate dataset used in any ML study of molecular adsorption in MOFs to date. Our workflow builds a benchmark for predicting Henry’s constants at 300 K, leveraging conformal prediction for uncertainty quantification. Assessment through Shannon entropy and uniform manifold approximation and projection confirms the comprehensiveness of D–MOPH–25 while highlighting the importance of robust classification to filter out unphysical data points in regression tasks. Although future enhancements in model architecture and sampling criteria could improve predictive performance, our dataset already spans the target space using only 2.31% of total possibilities. This comprehensive dataset facilitates assessment of model generalizability across adsorbate species and can establish a foundation for high-throughput MOF screening and ML-driven separation processes.

active learning↗
DOE OSTI2024

BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Abstract BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB’s positioning relative to related resources, its open data sharing policies, insights gleaned from the dataset and plans for future growth and development.

Liu, Tiqing↗
DOE OSTI2024

Ultrafast nuclear dynamics in double-core-ionized water molecules

Double-core-hole (DCH) states in isolated-water and heavy-water molecules, resulting from the sequential absorption of two x-ray photons, have been investigated. Here, a comparison of the subsequent Auger emission spectra from the two isotopes provides direct evidence of ultrafast nuclear motion during the 1.5-fs lifetime of these DCH states. Our numerical results align well with the experimental data, providing for various DCH states an in-depth study of the dynamics responsible of the observed isotope effect.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Transmission spectroscopy of CF 4 molecules in intense x-ray fields

The nonlinear interaction of x rays with matter is at the heart of understanding and controlling ultrafast molecular dynamics from an atom-specific viewpoint, providing new scientific and analytical opportunities to explore the structure and dynamics of small quantum systems. At increasingly high x-ray intensity, the sensitivity of ultrashort x-ray pulses to specific electronic states and emerging short-lived transient intermediates is of particular relevance for our understanding of fundamental multiphoton absorption processes. In this work, intense x-ray free-electron laser (XFEL) pulses at the European XFEL are combined with a gas cell and grating spectrometer for a high-intensity transmission spectroscopy study of multiphoton-induced ultrafast molecular fragmentation dynamics in CF 4 . This approach unlocks the direct intrapulse observation of transient fragments, including neutral atoms, by their characteristic absorption lines in the transmitted broadband x-ray spectrum. The dynamics with and without initially producing fluorine 𝐾-shell holes are studied by tuning the central photon energy. The absorption spectra are measured at different FEL intensities to observe nonlinear effects. Transient isolated fluorine atoms and ions are spectroscopically recorded within the ultrashort pulse duration of a few tens of femtoseconds. An isosbestic point that signifies the correlated transition between intact neutral CF 4 molecules and charged atomic fragments is observed near the fluorine 𝐾 edge. The dissociation dynamics and the multiphoton absorption-induced dynamics encoded in the spectra are theoretically interpreted. Overall, this study demonstrates the potential of high-intensity x-ray transmission spectroscopy to study ultrafast molecular dynamics with sensitivity to specific intermediate species and their electronic structure.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Production of meson molecules in ultraperipheral heavy ion collisons

In this work we present a calculation of exotic charmonium production in ultraperipheral collisions, in which the exotic state is explicitly treated as a meson molecule. Our formalism is general, but we focus on the lightest possible exotic charmonium state: a 𝐷 + ⁢𝐷 − molecular bound state. It was proposed some time ago, and it has been an object of experimental searches. Here we study the production of the open charm pair in the process 𝛾⁢𝛾 → 𝐷 + ⁢𝐷 − . Then we use a prescription to project the free pair |𝐷 + ⁢𝐷 − ⟩ onto a bound state at the amplitude level and compute the cross section of the process 𝛾⁢𝛾 → 𝐵 (where 𝐵 is the bound state). Finally, we convolute this last cross section with the equivalent photon distributions coming from the projectile and target in an ultraperipheral collision and find the 𝐴⁢𝐴 → 𝐴⁢𝐴⁢𝐵 cross section, which, for 𝑃⁢𝑏 −𝑃⁢𝑏 collisions at $\sqrt{s_{NN}}$ =5.02 TeV, is of the order of 3 μ⁢b.

Sobrinho, F. C.↗
DOE OSTI2025

Fast event-based electron counting for small-molecule structure determination by MicroED

Electron counting helped realize the resolution revolution in single-particle cryoEM and is now accelerating the determination of MicroED structures. Its advantages are best demonstrated by new direct electron detectors capable of fast (kilohertz) event-based electron counting (EBEC). This strategy minimizes the inaccuracies introduced by coincidence loss (CL) and promises rapid determination of accurate structures. We used the Direct Electron Apollo camera to leverage EBEC technology for MicroED data collection. Given its ability to count single electrons, the Apollo collects high-quality MicroED data from organic small-molecule crystals illuminated with incident electron beam flux densities as low as 0.01–0.045 e − /Å 2 /s. Under even the lowest flux density (0.01 e − /Å 2 /s) condition, fast EBEC data produced ab initio structures of a salen ligand (268 Da) and biotin (244 Da). Each structure was determined from a 100° wedge of data collected from a single crystal in as few as 50 s, with a delivered fluence of only ∼0.5 e − /Å 2 . Fast EBEC data collected with a fluence of 2.25 or 3.33 e − /Å 2 also facilitated a 1.5 Å structure of thiostrepton (1665 Da). While refinement of these structures appeared unaffected by CL, a CL adjustment applied to EBEC data further improved the distribution of intensities measured from the salen ligand and biotin crystals. However, CL adjustment only marginally improved the refinement of their corresponding structures, signaling the already high counting accuracy of detectors with counting rates in the kilohertz range. Overall, by delivering low-dose structure-worthy data, fast EBEC collection strategies open new possibilities for high-throughput MicroED.

EBEC↗
DOE OSTI2025

Q -score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps

Atomic coordinate models are important for the interpretation of 3D maps produced with cryoEM and cryoET (3D electron microscopy; 3DEM). In addition to visual inspection of such maps and models, quantitative metrics can inform about the reliability of the atomic coordinates, in particular how well the model is supported by the experimentally determined 3DEM map. A recently introduced metric, Q-score, was shown to correlate well with the reported resolution of the map for well fitted models. Here, we present new statistical analyses of Q-score based on its application to ∼10 000 maps and models archived in the EMDB (Electron Microscopy Data Bank) and PDB (Protein Data Bank). Further, we introduce two new metrics based on Q-score to represent each map and model relative to all entries in the EMDB and those with similar resolution. We explore through illustrative examples of proteins, nucleic acids and small molecules how Q-scores can indicate whether the atomic coordinates are well fitted to 3DEM maps and also whether some parts of a map may be poorly resolved due to factors such as molecular flexibility, radiation damage and/or conformational heterogeneity. These examples and statistical analyses provide a basis for how Q-scores can be interpreted effectively in order to evaluate 3DEM maps and atomic coordinate models prior to publication and archiving.

B factors↗
DOE OSTI2025

Use of Split‐Intein Proteins to Design a Small Molecule Biosensor in Plants

Understanding how plants perceive their environment is fundamental to advancing agricultural productivity and sustainability. Many biological small molecules, including those involved in microbial recognition, act rapidly at the plant cell surface, but the absence of tools to visualise these dynamics has limited our ability to dissect plant–microbe communication. To address this gap, we sought to create a genetically encoded biosensor that couples ligand-induced protein dimerization with the production of a fluorescent reporter. Inteins are peptide regions that excise themselves from precursor proteins and ligate the flanking chains (exteins). When each half of a split intein is fused to one of two dimerizing proteins, ligand binding brings them into proximity, inducing intein splicing and ligation of flanking extein sequences (Kang et al. 2022). Similar to previous studies, we split the yeast vacuolar ATPase subunit 1 (VMA1) intein, creating a protein biosensor that produces eGFP upon protein dimerization after ligand binding (Figure 1A) (Mootz et al. 2003). Specifically, eGFP halves (i.e., non-functional N- and C-terminal GFP fragments) were fused to the intein halves, resulting in two fusion proteins: N-terminal GFP::N-terminal intein and C-terminal intein::C-terminal GFP (Figure 1A).

Boone, Brandon A. [Oak Ridge National Laboratory (↗
DOE OSTI2025

Contribution to Open Molecules Dataset (coordcomplexsampling)

The Open Molecules Dataset is a project led by external collaborators, focused on the production of a wide diversity of molecular chemistries. This project will include high-throughput electronic structure calculations on metal coordination complexes, biomolecules, and electrolytes. Solvation effects, conformers, chemical reactivity, and spin/charge sampling will be pursued for elements on the periodic table up to, but not including the actinides. We aim to contribute code related to sampling for transition metal complexes, in particular, and expand software capabilities related to other thrusts desired.

Taylor, Michael G. [Los Alamos National Laboratory↗
DOE OSTI2026

Viral Nuclease Inhibitors: Small molecule disruptors of the UL12 alkaline nuclease display broad anti-herpes virus activity

Herpes simplex virus 1 (HSV-1) UL12 encodes a highly conserved 5′ → 3′ alkaline exonuclease that is essential for the production of infectious virus. Together with the viral single-stranded DNA-binding/annealing protein ICP8, UL12 functions as a two-component recombinase that mediates recombination-dependent viral DNA replication. Here, we present the crystal structure of the catalytic domain of the HSV alkaline nuclease (UL12), which provides the first view of an α-herpesvirus alkaline nuclease. Using this structure, we optimized a series of small-molecule viral nuclease inhibitors (VNIs) that target the UL12 active site and potently inhibit UL12 exonuclease activity in vitro. We have thus established a robust platform for structure-based docking, SAR analysis and rational inhibitor design. Because UL12 orthologs are conserved across all human herpesviruses, we examined the activity of these compounds against the β- and γ-herpesvirus alkaline nucleases UL98 and SOX and found that they inhibit all three enzymes. The VNIs also exhibit antiviral activity against HSV-1 and HCMV in cell culture. EC 50 and IC 50 values were in the nanomolar to low micromolar range. Together, these findings establish herpesvirus alkaline nucleases as conserved, druggable antiviral targets and provide a foundation for the development of broad-spectrum anti-herpesvirus therapeutics, either as standalone agents or in combination with existing nucleoside analogs.

Sharma, Nidhi↗
DOE OSTI2026

Chemical Recommender System: Replacement Suggestions for Small Molecules

The Chemical Recommender System (CRS) is an open-source, high-performance toolkit that enables real-time similarity searches across the complete PubChem database (over 50 million molecules) using commodity hardware. The CRS addresses critical limitations in existing chemical informatics platforms through a novel vector database infrastructure, extensible model integration capabilities, and complete algorithmic transparency. The system implements a vector database deployment with partitioned indexing that achieves a ~60x speedup over traditional approaches. A containerized model integration framework allows researchers to seamlessly incorporate custom predictive models into the full-scale search and scoring pipeline, while complete configurability of search parameters, filtering logic, and scoring functions provides capabilities not available in existing black-box solutions. Beyond structural similarity, the CRS integrates OPERA QSAR models for thermophysical and toxicity predictions, RDKit synthetic accessibility scoring, and user-defined models to compute weighted final replacement scores. The complete system is accessible through an interactive web application supporting real-time progress monitoring, post-processing score re-weighting, automated PDF reporting, and batch processing capabilities.

Nair, Parthiv Anand [Sandia National Laboratories ↗
DOE OSTI2026

Refined Sensitivity Estimates for Single-Molecule Magnet Dark Matter Detectors

We revisit the sensitivity of Single Molecule Magnet (SMM) crystals as detectors for low-mass dark matter. In previous work, we established the concept of the ``magnetic bubble chamber'', where energy deposited by dark matter triggers a magnetic avalanche in a metastable crystal. The original sensitivity estimates relied on a conservative criterion requiring the spin relaxation time to be strictly shorter than the thermal diffusion time. Here, we demonstrate that this criterion effectively ignores the stochastic nature of spin relaxation. We derive a refined analytic estimate which accounts for the fraction of spins that relax even when diffusion is fast. We show that the Zeeman energy released by this fraction contributes to local heating, significantly lowering the energy threshold for avalanche formation. We present simulation results confirming this effect and report on experimental verification of the assumed low-temperature thermal properties of two representative SMM crystals, Mn$_{12}$-acetate and Mn$_{32}$. Together, these efforts extend this pathfinder program toward the realization of SMM-based detectors with controlled material properties and enhanced dark matter sensitivity.

Eberhardt, Andrew [Tokyo U., IPMU]↗
DOE OSTI2025

A Theory of Ultrafast Charge Transfer Relaxation with Non-Innocent Solvent Molecules

In this work we revisit the photodynamics of tetracyanoethylene-hexamethylbenzene (TCNE- HMB), the molecular complex studied by Hochstrasser et al. [J. Chem. Phys. 100, 4797–4810, 1994] that has long challenged the applicability of Marcus’s theory of elec- tron transfer for predicting photochemical reactions. Using a novel black-box electronic structure algorithm (time-dependent density functional theory with one double, TD- DFT-1D) to efficiently run molecular dynamics that can treat charge recombination, we run ab initio surface hopping molecular dynamics and confirm that, for a polar solvent, charge recombination rates can be incredibly fast (indeed faster than the sol- vent relaxation time); for non-polar solvents, the rate is much slower. We demonstrate that, although Marcus theory cannot be directly applied, these nonequilibrium (and sometimes incredibly fast) photoexcited dynamics can be effectively explained within a two-state model without any evidence of a transition through a conical intersection. Most importantly, for this paradigmatic model system, we are able to identify two nuclear coordinates of interest (rather than the single coordinate predicted by Marcus or a full set of internal quantum modes studied by Bixon and Jortner): the solvent relaxation in the first shell (that strongly modulates the energies of the charge trans- fer state and differentiates time scales for relaxation) and a nuclear displacement in the TCNE-HMB complex arising from a handful of vibrations that induces non-Born Oppenheimer motion and eventually facilitates an abrupt electronic transition to the ground state. Altogether, these findings suggest a tractable generalization of Marcus theory for future simulations of photochemistry with non-innocent solvent environ- ments in the spirit of a Hamiltonian suggested by Stuchebrukhov (J. Chem. Phys. 107, 3821, 1997).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗