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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Selective Adsorption of Thiol-Containing Molecules on Copper Sulfide Surfaces via Molecule–Surface Disulfide Bridges

Recent results in the fields of nanoenhanced agriculture and expanding interest in prebiotic chemistry have placed increased emphasis on understanding the chemically selective interaction of small molecules with the surfaces of metal sulfides. Here, we present an integrated experimental and computational study of the interaction of thiol-containing molecules with copper sulfide (covellite) surfaces in aqueous media. In situ Fourier-transform infrared (FTIR) measurements and ex situ X-ray photoelectron spectroscopy (XPS) measurements show that molecules bearing free thiol groups, including glutathione and cysteine, bind strongly to CuS (covellite) nanoparticles and to CuS (001) single crystals, while control studies show that similar molecules lacking the free thiol group exhibit much less binding. Additional experiments show that these thiol-containing molecules interact transiently with CuO nanoparticle surfaces but are readily removed by rinsing. The FTIR and XPS experiments demonstrate that adsorption of molecular thiols to CuS surfaces occurs in a chemically selective manner. Further experimental studies and density functional calculations show that the preferred mode of binding is through the surface S atoms, forming a Solid–S–S–Molecule disulfide linkage. While the role of disulfide linkages in controlling structure and function of proteins and other biomolecules is widely known, the formation of surface disulfide linkages as a motif for covalent molecular binding at surfaces has not been established previously.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Discovery of Signaling Small Molecules (e.g. quorum sensing molecules) from the Microbiome

Microbial communities are shaped through the interactions between their microbial members and the environment (microbe-microbe and host-microbe interactions). Signal transduction pathways in the microbiome are often modulated through the small molecule products of microbial biosynthetic gene clusters (BGCs). Advances in 16S rRNA profiling and shotgun metagenomics have revolutionized our understanding about the microbial composition of various communities and their BGCs. Environmental metagenomes contain thousands of BGCs with uncharacterized small molecule products that potentially play roles in signal transduction. The overarching aim of this proposal was to develop computational techniques for discovering these small molecules and characterizing their bioactivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Super-Resolved Single-Molecule Tracking Studies of Rhodamine B Accumulation on Fresh and Aged Polyethylene Terephthalate

It is well-known that toxic organic micropollutants (OMs) accumulate on the surfaces of microplastics. However, much remains to be learned about the exact molecular level mechanisms of OM accumulation and how these evolve as the plastics age. In this work, super-resolved single-molecule tracking (SMT) is used for the first time to investigate the accumulation of Rhodamine B (RhB) dye on fresh and artificially aged polyethylene terephthalate (PET) surfaces. PET thin films serve as models for microplastics, while RhB serves as a proxy for the OMs they accumulate. Artificial aging of the films is accomplished by exposing them in a UV-ozone chamber. Water contact angle, spectroscopic ellipsometry, and carbonyl index measurements reveal a gradual decrease in film hydrophobicity, thickness, and carbonyl content with age. Atomic force microscopy (AFM) data reveal an increase in surface roughness and confirm that the films remain largely intact and continuous across the aging times explored. In SMT experiments, wide-field fluorescence videos acquired from the water/PET interface under 7.5 pM RhB reveal both mobile and immobile dye molecules. Measurements of the frame-to-frame displacements of the dye show that diffusion occurs by a desorption-mediated mechanism and that the diffusion rate varies with PET film age. The surface density of mobile dye molecules decreases with increasing PET age, while the population of immobile molecules becomes relatively larger, suggesting an age-dependent transformation of the mechanism(s) by which the dye is accumulated. SMT data reveal that both mobile and immobile molecules repeatedly adsorb over the same surface sites, consistent with the emergence of nanoscale PET surface heterogeneity also revealed by AFM. Estimates of the adsorption coefficients are obtained using a nearest-neighbor analysis, giving values from 9.9 × 10 5 to 2.1 × 10 6 M –1 for immobile molecules and from 1.8 × 10 5 to 2.5 × 10 5 M –1 for mobile molecules on fresh and 5 min aged PET, respectively. Here, anomalous age-dependent variations in the velocity of molecular motion on the PET surface and in the population of immobile molecules are shown to correlate with changes in the strength of RhB adsorption.

Adsorption↗
DOE OSTI2025

Electrochemically modulated single-molecule localization microscopy for in vitro imaging cytoskeletal protein structures

A new concept of electrochemically modulated single-molecule localization super-resolution imaging is developed. Applications of single-molecule localization super-resolution microscopy have been limited due to insufficient availability of qualified fluorophores with favorable low duty cycles. The key for the new concept is that the “On” state of a redox-active fluorophore with unfavorable high duty cycle could be driven to “Off” state by electrochemical potential modulation and thus become available for single-molecule localization imaging. The new concept was carried out using redox-active cresyl violet with unfavorable high duty cycle as a model fluorophore by synchronizing electrochemical potential scanning with a single-molecule localization microscope. The two cytoskeletal protein structures, the microtubules from porcine brain and the actins from rabbit muscle, were selected as the model target structures for the conceptual imaging in vitro. The super-resolution images of microtubules and actins were obtained from precise single-molecule localizations determined by modulating the On/Off states of single fluorophore molecules on the cytoskeletal proteins via electrochemical potential scanning. Importantly, this method could allow more fluorophores even with unfavorable photophysical properties to become available for a wider and more extensive application of single-molecule localization microscopy.

electrochemical modulation↗
DOE OSTI2026

Active learning enables generation of molecules that advance the known Pareto front

Although generative models hold promise for discovering molecules with optimized desired properties, they often fail to suggest synthesizable molecules that improve upon the properties of the structures represented in the training distribution. We find that this limitation arises not only from the molecule generation process itself, but also from the poor generalization capabilities of molecular property predictors. We address this challenge by creating a closed-loop molecule generation pipeline with iterative retraining on new quantum chemical simulation data. Compared against static, single-pass generative modeling approaches, only our closed-loop iterative workflow generates molecules with properties extending beyond the training distribution (up to 0.44 standard deviations beyond the original range) and achieves a 79% improvement in out-of-distribution molecule classification accuracy. Furthermore, by conditioning molecular generation on thermodynamic stability data obtained during the iterative loop, the proportion of stable and hence potentially synthesizable molecules generated is 3.5x higher than the next-best model.

Chemistry↗
DOE OSTI2026

Discovery of hydrogen storage molecules using large language models and machine learning

Accelerating the discovery of new molecules with targeted properties is a central challenge in molecular design. In this contribution, we present an AI-driven molecular discovery framework that integrates Large Language Models (LLMs) for generative molecular design with Machine Learning (ML)-based screening to identify novel Liquid Organic Hydrogen Carrier (LOHC) candidates. Using the developed framework, LOHC molecules were systematically generated, evaluated, and refined iteratively, combining LLM-guided molecular generation and ML-predicted hydrogenation enthalpies (Δ H ), under physicochemical property constraints such as optimal melting points (MP), desired hydrogen storage capacity (wt% H 2 ), and synthetic accessibility (SA) scores. This approach enabled the discovery of 42 new LOHC candidates in two distinct campaigns, one seeded with experimentally known and another with previously computationally identified LOHCs, respectively. Although we began with different numbers of starting molecules (31 vs . 7 seed molecules), both runs yielded a comparable number of viable candidates, suggesting an influence of chemically intuitive seed molecule selection for success. Selected LOHC molecules, such as 3-methyl pyridine, 1-ethylnapthalene, 1,1-diphenylethane, and benzofuran, were experimentally tested and compared with benchmark LOHCs (toluene and 9-ethylcarbazole) for hydrogenation using a series of commercial supported metal catalysts. The order of conversion into fully hydrogenated products at 200 °C was 3-methyl pyridine (100%) > 9-ethyl carbazole (86.4%) > 2,3-benzofuran (74%) > 1,1-diphenylethane (66.9%) > 1-ethylnapthalene (66.7%) > toluene (57%), further validating the AI-guided molecular design. This study demonstrates promise of LLM-driven molecular design in conjunction with ML-based screening for accelerated discovery and design of molecules.

Harb, Hassan [Argonne National Laboratory (ANL), A↗
DOE OSTI2026

Parity-doublet coherence times in optically trapped polyatomic molecules

Polyatomic molecules provide complex internal structures that are ideal for applications in quantum information science, quantum simulation and precision searches for physics beyond the standard model. A key feature of polyatomic molecules is the presence of parity-doublet states. These structures, which generically arise from the rotational and vibrational degrees of freedom afforded by polyatomic molecules, are a powerful feature to pursue diverse quantum science applications. Linear triatomic molecules contain ℓ-type parity-doublet states in the vibrational bending mode, which are predicted to exhibit robust coherence properties. Here we report optically trapped CaOH molecules prepared in ℓ-type parity-doublet states and realize a bare qubit coherence time of $T$$^{*}_{2}$, which is longer than the 0.36 s lifetime of the bending mode. We suppress differential Stark shifts by cancelling ambient electric fields using molecular spectroscopy and characterize parity-dependent trap shifts, which are found to limit the coherence time. Furthermore, the parity-doublet coherence times achieved in this work are a defining milestone for the use of polyatomic molecules in quantum science.

Quantum information↗
DOE OSTI2025

Conjugation effect of amine molecules in non-aqueous Mg redox flow batteries

Nonaqueous magnesium redox flow batteries (Mg RFBs) are attractive for low-cost, high-energy-density and long-cycle-life stationary energy storage applications. However, state-of-the-art cathode redox-active molecules suffer from low solubility and low redox potential. Herein, we screened a range of cathode redox-active molecules and identified amine molecules as optimal to couple with the Mg anode. The properties of amine derivatives and their performances were collected to establish the correlation between molecular structures and electrochemical performances. The redox potential and solubility of these amine molecules were influenced by the π-conjugated and non-conjugated structures of amine derivatives. Density functional theory (DFT) simulations and the inverse aromatic fluctuation index (FLU −1 ) verified that conjugation had an important role in stabilizing the molecule and increasing its redox potential. Notably, tris[4-(diethylamino)phenyl]amine (TDPA) achieved the highest theoretical energy density (∼120 Wh L −1 ) due to its high solubility (∼0.9 M) and voltage (∼2.5 V vs. Mg/Mg 2+ ). We also demonstrated that ether solvents were crucial for stable, high-solubility catholytes, while bulk anions did not affect the redox potential of these p-type molecules. In a Mg-amine RFB configuration, the battery delivered 2.50 V, a specific discharge capacity of 106.5 mAh g −1 , an initial coulombic efficiency of 90.74%, and a capacity retention of 93.88% after 150 cycles.

Qin, Yunan [University of Utah, Salt Lake City, UT↗
DOE OSTI2025

Abnormal Slow Phonon Dynamics Toward Prolonging Excited States Dynamics Enabled by Crystalline‐Assembling Donor–Acceptor Molecules

Phonon dynamics are a critical factor to control the optical properties of excited states in light-emitting materials. Here, we report an extremely slow relaxation of photoexcited lattice vibrations enabled by assembling the donor-acceptor (D–A) molecules [2-(9,9-dimethylacridin-10(9H)-yl)-9,9-dimethyl-9H-thioxanthene 10,10-dioxide], namely AC molecules, into dipolar crystal. By using photoexcitation-modulated Raman spectroscopy, we find that the crystalline-lattice vibrations monitored by Raman-scattering laser beam of 785 nm demonstrate an un-usual slow relaxation in the time scale of seconds after ceasing photoexcitation beam of 343 nm in such dipolar crystal. This presents extremely slow phonon dynamics enabled by crystalline-assembling the D–A molecules into a dipolar crystal. Simultaneously, the photoluminescence (PL) exhibits a prolonged behavior, lasting 10 ms after ceasing photoexcitation in dipolar AC crystal. This phenomenon provides an experimental hypothesis that the slow phonon dynamics function as an important mechanism to unusually prolong excited states dynamics upon crystalline-assembling the D–A molecules into dipolar crystal. Here, this hypothesis can be verified by directly suppressing the phonon dynamics through freezing D–A molecular liquid into dipolar crystalline solid at 77 K to largely prolong the PL to 1 s- after removing photoexcitation. Clearly, crystalline-assembling D–A molecules provide the necessary conditions to enable slow phonon dynamics toward prolonging excited states dynamics.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Single-Molecule Tracking Measurements Reveal the Detailed Mechanisms of Molecular Diffusion in Solvent Mixtures under Nanoconfinement

Understanding mass transport mechanisms in nanopores is important for developing advanced materials for chemical separations, chemical sensing, and energy storage. This paper reports a novel imaging platform that is employed for the first time to investigate the detailed diffusion dynamics of single rhodamine B (RhB) dye molecules confined within solution-filled cylindrical anodic aluminum oxide (AAO) nanopores. The imaging platform relies on illumination of horizontally-oriented AAO nanopores in a highly inclined and laminated optical (HILO) light sheet microscopy geometry. The method was used to investigate the translational and orientational dynamics of single rhodamine B (RhB) molecules within horizontally-oriented 5- and 10-nm diameter AAO nanopores filled with water–ethanol mixtures. The established platform enabled the observation of one-dimensional motion along the pore axis involving occasional short- or long-term immobilization at the single-molecule level. Analysis of cumulative squared-displacement distributions revealed fast (5 – 30 µm²/s), intermediate (1 – 5 µm²/s), and slow (< 1 µm²/s) diffusion components. From the effects of mixture composition and pore size on the contributions of these three components, we inferred that the fast, intermediate, and slow components could be assigned to desorption-mediated hopping, crawling, and wiggling motions, respectively. The platform based on the horizontally-oriented AAO nanopores also permitted single-molecule emission polarization measurements that revealed the negligible steric confinement of individual diffusing RhB molecules within the AAO nanopores. The imaging platform based on AAO membranes and HILO microscopy provided a unique means to investigate how solvation-mediated surface interactions and nanoconfinement govern molecular transport in nanoporous environments.

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

Probing Dipolar Interactions between Rydberg Atoms and Ultracold Polar Molecules

Here, we probe resonant dipolar interactions between ultracold 40 K ⁢ 87 Rb molecules and Rydberg 87 Rb atoms in an optically trapped ensemble. Through state-selective ionization detection of the KRb molecules, we observe resonant energy transfer at 2.227 GHz from Rydberg atoms to molecules under a tunable external electric field. We measure a broadening up to 3.5 MHz, for the Rb Rydberg excitation spectrum, which matches a Monte Carlo simulation that describes a Rydberg atom and neighboring molecules evolving under a dipole-dipole interacting Hamiltonian. The demonstrated interspecies dipolar interaction is a key ingredient for hybrid Rydberg-polar molecule systems, where the advantages of each system can be leveraged and combined.

dipolar Rydberg atoms↗
DOE OSTI2025

Layers Can Be Deceiving: A Hopping Model for Small Molecule Diffusion in TATB Crystal

Sorption of small molecule gases in materials can play a significant role in their long‐term stability and compatibility within multi‐material assemblies. While many material properties of the insensitive high explosive TATB (1,3,5‐triamino‐2,4,6‐trinitrobenzene) are well understood, very little is known regarding its permeability to gases. TATB crystal exhibits a graphitic‐like layered packing structure that evokes a mental schema in which the layers form nanoscopic channels, but it is unclear whether this structure promotes gas transport. Here, we use molecular dynamics (MD) simulations to predict transport of small molecules through TATB single crystal. An approach to fit classical force fields is developed to model TATB interactions with H 2 O, He, Ne, and Ar, which is then combined with steered MD to probe gas transport along selected directions in the crystal. We find that small molecule transport occurs via a hopping mechanism that exhibits distinct jumps between interstitial sites and is substantially faster normal to the layers as compared to through them. This result stems from the finding that intralayer junctions between adjacent TATB molecules are the most stable interstitial sites and that energetic barriers are lower for hopping between adjacent layers. An empirical model for diffusion rate based on the MD data shows that the rate decays exponentially with increasing molecular radius and is negligibly small for all molecules larger than He, including common atmospheric gases. These findings have implications for the interpretation of experiments that measure surface area, material response to extreme conditions, and are expected to help constrain models for material aging.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Precision ultranarrow-linewidth resonance excitation (PURE) preparation of a molecular beam of nitric oxide molecules for inelastic scattering with argon

We recently reported a novel technique that utilizes narrow-linewidth lasers to selectively excite molecules into a pure quantum state with a well-resolved, tunable distribution of velocities [O. A. Krohn and D. W. Chandler, J. Phys. Chem. Lett. 15(50), 12455–12463 (2024)]. We refer to the preparation of molecules by this technique as precision ultranarrow-linewidth resonant excitation (PURE) preparation. Here, in this study, we pair this PURE preparation methodology with active frequency stabilization of the quantum cascade laser that drives the excitation. In doing so, highly velocity-resolved packets of molecules are possible, with the limitations of this velocity resolution set by the stability of the laser locking and the spectral linewidth of the transition. We show that side-of-fringe locking to a Doppler-broadened absorption spectrum of our target molecule is sufficiently stable for PURE preparation of molecules for long timescales (several hours) with highly resolved velocity spreads (σ < 3 m/s). To demonstrate the scientific utility of this new capability, we present differential cross sections from scattering between a neat molecular beam of argon and a velocity-selected beam of nitric oxide (NO) in a pure quantum state. We observe well-resolved quantum diffraction oscillations in the forward-scattered collisions as well as general trends consistent with prior characterized collisions of NO + Ar.

Krohn, Olivia A. [Sandia National Laboratories (SN↗
DOE OSTI2025

CSGL: chemical synthesis graph learning for molecule representation

Abstract Motivation Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. Results Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation https://github.com/li-2023/CSGL.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Quantum-State-Controlled Collisions of Ultracold Polyatomic Molecules

Collisions between ultracold calcium monohydroxide (CaOH) molecules are realized and studied. Inelastic collision rate constants are measured for CaOH prepared in ground and excited vibrational states, and the electric field dependence of these rates is measured for molecules in single quantum states of the parity-doubled bending mode. Theoretical calculations of collision rate coefficients are performed and found to agree with measured values. The lowest collisional loss rates are for states with repulsive long-range potentials that shield ultracold molecules from loss channels at short distance. These results unveil the collisional behavior of parity-doublet molecules in the ultracold regime and lay the foundation for future experiments to evaporatively cool polyatomic molecules to quantum degeneracy.

Vilas, Nathaniel B. [Harvard University, Cambridge↗
DOE OSTI2025

Observation of the distribution of nuclear magnetization in a molecule

Precise experimental control and interrogation of molecules and calculations of their structure are enriching the investigation of nuclear and particle physics phenomena. Molecules containing heavy, octupole-deformed nuclei, such as radium, are of particular interest. Here, we report precision laser spectroscopy measurements and theoretical calculations of the structure of the radioactive radium monofluoride molecule 225 Ra 19 F. Our results reveal fine details of the short-range electron-nucleus interaction, indicating the high sensitivity of this molecule to the distribution of magnetization, within the radium nucleus. Here, these results provide a stringent test of the description of the electronic wave function inside the nuclear volume, highlighting the suitability of these molecules for investigating subatomic phenomena.

Nuclear structure↗
NASA NTRS2026

Diverse organic molecules on Mars revealed by the first SAM TMAH experiment

The search for organic matter on Mars has rapidly evolved in the past decade with simple aromatic, S-heterocycles, and aliphatic organic molecules detected in Gale crater. We report the in situ detection of >20 organic molecules from clay-bearing sandstones in the ~3.5-billion-year-old Knockfarrill Hill member of Glen Torridon, Gale crater, by the Sample Analysis at Mars instrument suite onboard the Curiosity rover. These molecules were liberated by the onboard tetramethylammonium hydroxide wet chemistry experiment. Diverse thermochemolysis products, including benzothiophene, methyl benzoate, and single and dicyclic aromatic molecules were released and detected by evolved gas analysis and gas chromatography-mass spectrometry. Results indicate the experiment successfully released molecules preserved in ancient macromolecular or free organic matter within Martian bedrock despite ~3.5 billion years of diagenesis and radiation exposure.

Amy J Williams↗
DOE OSTI2025

Single-Molecule Conductance through Hybrid Radially and Linearly π-Conjugated Macromolecules Reveals an Unusual Intramolecular π-Interaction

We describe the design, synthesis, and single-molecule junction conductance of π-electron molecules bearing both radial and linear π-conjugation pathways, whereby cycloparaphenylene (CPP) radial cores are π-extended linearly with aryl alkyne substituents as models for previously reported CPP-arylene ethynylene conjugated polymers. Although radially and linearly conjugated molecules have been studied previously in isolation as junction-bridging molecular electronic units, this is the first study to examine molecules where both topologies are operative. Our results reveal that the presence of radial CPP components within the junction-spanning pathway leads to a reduction in the conductance of the backbone compared to model linear phenyl substituents. Through tight-binding and DFT-based calculations, we attribute this conductance change to intramolecular van der Waals (vdW) interactions between the CPP ring and the junction-spanning arylene-ethynylene molecular backbone. These interactions induce changes in the dihedral angles of the backbone, leading to a reduced overlap of π orbitals within the molecular junction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗