Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “MOLECULES”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 901 records · Page 50
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Energy-efficient pathway for selectively exciting solute molecules to high vibrational states via solvent vibration-polariton pumping

Abstract Selectively exciting target molecules to high vibrational states is inefficient in the liquid phase, which restricts the use of IR pumping to catalyze ground-state chemical reactions. Here, we demonstrate that this inefficiency can sometimes be solved by confining the liquid to an optical cavity under vibrational strong coupling conditions. For a liquid solution of 13 CO 2 solute in a 12 CO 2 solvent, cavity molecular dynamics simulations show that exciting a polariton (hybrid light-matter state) of the solvent with an intense laser pulse, under suitable resonant conditions, may lead to a very strong (>3 quanta) and ultrafast (<1 ps) excitation of the solute, even though the solvent ends up being barely excited. By contrast, outside a cavity the same input pulse fluence can excite the solute by only half a vibrational quantum and the selectivity of excitation is low. Our finding is robust under different cavity volumes, which may lead to observable cavity enhancement on IR photochemical reactions in Fabry–Pérot cavities.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Incoherent nonadiabatic to coherent adiabatic transition of electron transfer in colloidal quantum dot molecules

Electron transfer is a fundamental process in chemistry, biology, and physics. One of the most intriguing questions concerns the realization of the transitions between nonadiabatic and adiabatic regimes of electron transfer. Using colloidal quantum dot molecules, we computationally demonstrate how the hybridization energy (electronic coupling) can be tuned by changing the neck dimensions and/or the quantum dot sizes. This provides a handle to tune the electron transfer from the incoherent nonadiabatic regime to the coherent adiabatic regime in a single system. We develop an atomistic model to account for several states and couplings to the lattice vibrations and utilize the mean-field mixed quantum-classical method to describe the charge transfer dynamics. Here, we show that charge transfer rates increase by several orders of magnitude as the system is driven to the coherent, adiabatic limit, even at elevated temperatures, and delineate the inter-dot and torsional acoustic modes that couple most strongly to the charge transfer dynamics.

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

Identification and characterization of small molecule inhibitors of the LINE-1 retrotransposon endonuclease

The long interspersed nuclear element-1 (LINE-1 or L1) retrotransposon is the only active autonomously replicating retrotransposon in the human genome. L1 harms the cell by inserting new copies, generating DNA damage, and triggering inflammation. Therefore, L1 inhibition could be used to treat many diseases associated with these processes. Previous research has focused on inhibition of the L1 reverse transcriptase due to the prevalence of well-characterized inhibitors of related viral enzymes. Here we present the L1 endonuclease as another target for reducing L1 activity. We characterize structurally diverse small molecule endonuclease inhibitors using computational, biochemical, and biophysical methods. We also show that these inhibitors reduce L1 retrotransposition, L1-induced DNA damage, and inflammation reinforced by L1 in senescent cells. These inhibitors could be used for further pharmacological development and as tools to better understand the life cycle of this element and its impact on disease processes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Fluorescence imaging of individual ions and molecules in pressurized noble gases for barium tagging in 136Xe

Abstract The imaging of individual Ba 2+ ions in high pressure xenon gas is one possible way to attain background-free sensitivity to neutrinoless double beta decay and hence establish the Majorana nature of the neutrino. In this paper we demonstrate selective single Ba 2+ ion imaging inside a high-pressure xenon gas environment. Ba 2+ ions chelated with molecular chemosensors are resolved at the gas-solid interface using a diffraction-limited imaging system with scan area of 1 × 1 cm 2 located inside 10 bar of xenon gas. This form of microscopy represents key ingredient in the development of barium tagging for neutrinoless double beta decay searches in 136 Xe. This also provides a new tool for studying the photophysics of fluorescent molecules and chemosensors at the solid-gas interface to enable bottom-up design of catalysts and sensors.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Bridging the gap between molecules and materials in quantum chemistry with localized active spaces

The number of materials that “bridge the gap” between single molecules and extended solids, such as metal-organic frameworks and organic semiconductors, has been increasing. Consequently, there is a growing need for modeling approaches that effectively integrate the real-space molecular perspective employed by computational chemists and the reciprocal-space dispersive perspective employed by computational physicists. Here, we propose the localized active space (LAS) approach as a promising method to successfully bridge this gap. The LAS approach extends the active space concept from multiconfigurational methods such as complete active space self-consistent field theory to multiple molecular fragments via a product-form wave function ansatz. Here, we apply this method to solid state phenomena by treating each unit cell as a fragment with different sets of local quantum numbers (e.g., charge and excitation number). State interaction between these LAS states (LASSI) thus provides a comprehensive basis for the study of charge and energy transfer, meeting and surpassing the capabilities of single-reference fragmentation approaches such as constrained density functional theory (cDFT). Most centrally, we show how combining this LASSI approach with multiconfigurational pair-density functional theory (MC-PDFT) provides an elegant and efficient method to compute band structures that capture multiconfigurational character. We apply the LASSI band structure approach to the computation of band gaps in stretched hydrogen chain, polyacetylene, and bulk nickel oxide (NiO), finding good or excellent quantitative agreement with reference values in all cases. Additionally, we use the LAS basis in one-dimensional model systems to demonstrate its ability to treat difficult solid-state phenomena such as exciton transfer and excitation at p-n junctions.

method development↗
DOE OSTI2026

Small-molecule modulation of β-arrestins

β-Arrestins are multifunctional regulators of G-protein-coupled receptor (GPCR) signalling and orchestrate diverse downstream signalling events and physiological responses across the GPCR superfamily. Although GPCR pharmacology has advanced to target orthosteric and allosteric sites, as well as G proteins and GPCR kinases, direct chemical tools to modulate β-arrestin activities have remained conspicuously absent. Here we report the identification of small-molecule inhibitors that selectively target β-arrestins and delineate their mechanism of action through integrated pharmacological, biochemical, biophysical and structural analyses. These inhibitors disrupt β-arrestin engagement with agonist-activated GPCRs, impairing desensitization, internalization and β-arrestin-dependent physiological functions while sparing G protein–receptor coupling. Cryo-electron microscopy, molecular dynamics simulations and structure-guided mutagenesis reveal that one modulator, Cmpd-5, engages a pocket within the central crest of β-arrestin1 formed by the middle, C and lariat loops, a critical receptor-binding interface, stabilizing a distinct conformation that is incompatible with full β-arrestin–receptor engagement. Together, these findings establish a mechanistic framework for β-arrestin modulation, reveal a novel allosteric site for structure-based drug design, and open new avenues for transducer-targeted, pathway-specific GPCR therapeutic agents.

Kahsai, Alem W. [Duke University, Durham, NC (Unit↗
DOE OSTI2022

A small molecule inhibitor prevents gut bacterial genotoxin production

Abstract The human gut bacterial genotoxin colibactin is a possible key driver of colorectal cancer (CRC) development. Understanding colibactin’s biological effects remains difficult owing to the instability of the proposed active species and the complexity of the gut microbiota. Here, we report small molecule boronic acid inhibitors of colibactin biosynthesis. Designed to mimic the biosynthetic precursor precolibactin, these compounds potently inhibit the colibactin-activating peptidase ClbP. Using biochemical assays and crystallography, we show that they engage the ClbP binding pocket, forming a covalent bond with the catalytic serine. These inhibitors reproduce the phenotypes observed in a clbP deletion mutant and block the genotoxic effects of colibactin on eukaryotic cells. The availability of ClbP inhibitors will allow precise, temporal control over colibactin production, enabling further study of its contributions to CRC. Finally, application of our inhibitors to related peptidase-encoding pathways highlights the power of chemical tools to probe natural product biosynthesis.

Biochemistry & Molecular Biology↗
DOE OSTI2020

The ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for molecules

Abstract Maximum diversification of data is a central theme in building generalized and accurate machine learning (ML) models. In chemistry, ML has been used to develop models for predicting molecular properties, for example quantum mechanics (QM) calculated potential energy surfaces and atomic charge models. The ANI-1x and ANI-1ccx ML-based general-purpose potentials for organic molecules were developed through active learning; an automated data diversification process. Here, we describe the ANI-1x and ANI-1ccx data sets. To demonstrate data diversity, we visualize it with a dimensionality reduction scheme, and contrast against existing data sets. The ANI-1x data set contains multiple QM properties from 5 M density functional theory calculations, while the ANI-1ccx data set contains 500 k data points obtained with an accurate CCSD(T)/CBS extrapolation. Approximately 14 million CPU core-hours were expended to generate this data. Multiple QM calculated properties for the chemical elements C, H, N, and O are provided: energies, atomic forces, multipole moments, atomic charges, etc. We provide this data to the community to aid research and development of ML models for chemistry.

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

A database of synthetic inelastic neutron scattering spectra from molecules and crystals

Abstract Inelastic neutron scattering (INS) is a powerful tool to study the vibrational dynamics in a material. The analysis and interpretation of the INS spectra, however, are often nontrivial. Unlike diffraction, for which one can quickly calculate the scattering pattern from the structure, the calculation of INS spectra from the structure involves multiple steps requiring significant experience and computational resources. To overcome this barrier, a database of INS spectra consisting of commonly seen materials will be a valuable reference, and it will also lay the foundation of advanced data-driven analysis and interpretation of INS spectra. Here we report such a database compiled for over 20,000 organic molecules and over 10,000 inorganic crystals. The INS spectra are obtained from a streamlined workflow, and the synthetic INS spectra are also verified by available experimental data. The database is expected to greatly facilitate INS data analysis, and it can also enable the utilization of advanced analytics such as data mining and machine learning. Notice: This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan ( http://energy.gov/downloads/doe-public-access-plan ).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

An ontology-based knowledge graph for representing interactions involving RNA molecules

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to each patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are constantly produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph (KG) encompassing biological knowledge about RNAs gathered from more than 60 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Quantum mechanical dataset of 836k neutral closed-shell molecules with up to 5 heavy atoms from C, N, O, F, Si, P, S, Cl, Br

Abstract We introduce the Vector-QM24 (VQM24) dataset comprehensively covering all possible neutral closed-shell small organic and inorganic molecules with up to five heavy (p-block) atoms: C, N, O, F, Si, P, S, Cl, Br. All valid stoichiometries, Lewis-rule-consistent graphs, and stable conformers (identified via GFN2-xTB) were enumerated combinatorially, yielding 577k conformational isomers spanning 258k constitutional isomers and 5,599 unique stoichiometries. DFT (ωB97X-D3/cc-pVDZ) optimizations were performed for all, and diffusion quantum Monte Carlo (DMC@PBE0(ccECP/cc-pVQZ)) energies are provided for 10,793 lowest-energy conformers with up to 4 heavy atoms. VQM24 includes structures, vibrational modes, rotational constants, thermodynamic properties (Gibbs free energies, enthalpies, ZPVEs, entropies, heat capacities), and electronic properties such as atomization, electron interaction, exchange-correlation, dispersion energies, multipole moments (dipole to hexadecapole), alchemical potentials, Mulliken charges, and wavefunctions. Machine learning models of atomization energies on this dataset reveal significantly higher complexity than QM9, with none achieving chemical accuracy. VQM24 offers a rigorous, high-fidelity benchmark for evaluating quantum machine learning models.

Science & Technology - Other Topics↗
DOE OSTI2020

Conjugated Polymer Controlled Morphology and Charge Transport of Small-Molecule Organic Semiconductors

In this study, we report an efective approach to tune the crystallization, microstructure and charge transport of solution-processed organic semiconductors by blending with a conjugated polymer additive poly(3-hexylthiophene) (P3HT). When 6,13-bis(triisopropylsilylethynyl) pentacene (TIPS pentacene) was used as a model semiconductor material to mix with diferent amount of P3HT, their intermolecular interactions led to distinctive TIPS pentacene flm morphologies, including randomly-oriented crystal ribbons, elongated needles with enhanced long-range order, and grasslike curved microwires with interlinkages. Each type of morphology was found to further correlate to considerably diferent charge transport and device performance. As compared to pristine TIPS pentacene devices, bottom-gate, top-contact OTFTs with 2% in weight P3HT additive showed a 2-fold and 5-fold improvement of average feld-efect mobility and performance consistency (defned as the ratio of average mobility to the standard deviation), respectively. The improvement in transistor electrical performance can be attributed to the combined efect of enhanced crystal orientation and uniformity, as well as increased areal coverage. This work can be applied beyond the particular example demonstrated in this study and to tune the charge transport of other small-molecule organic semiconductors in general.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Organic molecules are deterministically assembled in variably inundated river sediments, but drivers remain unclear

Dissolved organic matter (DOM) is central to ecosystem function. A fundamental challenge is understanding the processes leading to variation in the chemistry of organic molecules that comprise DOM. Here we study these processes in variably inundated riverbed sediments, as an understudied, yet ubiquitous component of rivers. Using null-model approaches adopted from community ecology, we found that within-site variation in environmental conditions caused non-random (i.e., deterministic) shifts in DOM chemistry. Deterministic shifts were observed across diverse biomes, though the strength of determinism varied substantially. We found that the strength of determinism decreased with increasing sediment moisture, but in the form of a constraint space. Many systems fell below the upper constraint boundary, however. We propose a conceptual model based on our results and other publications in which DOM assemblages are hypothesized to be increasingly deterministic across the continuum from the river water column to saturated sediment pore spaces to unsaturated and dry soils/sediments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The co-crystal structure of Cbl-b and a small-molecule inhibitor reveals the mechanism of Cbl-b inhibition

Cbl-b is a RING-type E3 ubiquitin ligase that is expressed in several immune cell lineages, where it negatively regulates the activity of immune cells. Cbl-b has specifically been identified as an attractive target for cancer immunotherapy due to its role in promoting an immunosuppressive tumor environment. A Cbl-b inhibitor, Nx-1607, is currently in phase I clinical trials for advanced solid tumor malignancies. Using a suite of biophysical and cellular assays, we confirm potent binding of C7683 (an analogue of Nx-1607) to the full-length Cbl-b and its N-terminal fragment containing the TKBD-LHR-RING domains. To further elucidate its mechanism of inhibition, we determined the co-crystal structure of Cbl-b with C7683, revealing the compound’s interaction with both the TKBD and LHR, but not the RING domain. Here, we provide structural insights into a novel mechanism of Cbl-b inhibition by a small-molecule inhibitor that locks the protein in an inactive conformation by acting as an intramolecular glue.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Electrically tuned hyperfine spectrum in neutral Tb( II )(Cp iPr5 ) 2 single-molecule magnet

Molecular spin qubits with long spin coherence time as well as non-invasive operation methods on such qubits are in high demand. It was shown that both molecular electronic and nuclear spin levels can be used as qubits. In solid state systems with dopants, an electric field was shown to effectively change the spacing between the nuclear spin qubit levels when the electron spin density is high at the nucleus of the dopant. Inspired by such solid-state systems, we propose that divalent lanthanide (Ln) complexes with an unusual electronic configuration of Ln 2+ have a strong interaction between the Ln nuclear spin and the electronic degrees of freedom, which renders electrical tuning of the interaction. Furthermore, as an example, we study electronic structure and hyperfine interaction of the 159 Tb nucleus in a neutral Tb(II)(Cp iPr5 ) 2 single-molecule magnet (SMM), which exhibits unusually long magnetization relaxation time, using the complete active space self-consistent field (CASSCF) method with spin–orbit interaction included within the restricted active space state interaction (RASSI). Our calculations show that the low-energy states arise from 4f 8 (6s,5d z 2 ) 1 , 4f 8 (5d x 2 -y 2 ) 1 , and 4f 8 (5d xy ) 1 configurations. We compute the hyperfine interaction parameters and the electronic–nuclear spectrum within our multiconfigurational approach. We find that the hyperfine interaction is about one order of magnitude greater than that for Tb(III)Pc 2 SMMs. This stems from the strong Fermi contact interaction between the Tb nuclear spin and the electron spin density at the nucleus that originates from the occupation of the (6s,5d) orbitals. We also uncover that the response of the Fermi contact term to electric field results in electrical tuning of the electronic–nuclear level separations. This hyperfine Stark effect may be useful for applications of molecular nuclear spins for quantum computing.

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

Efficiency analysis of helium-cooled MAS DNP: case studies of surface-modified nanoparticles and homogeneous small-molecule solutions

Despite the growing number of successful applications of dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) NMR in structural biology and materials science, the nuclear polarizations achieved by current MAS DNP instrumentation are still considerably lower than the theoretical maximum. Here, the method could be significantly strengthened if experiments were performed at temperatures much lower than those currently widely used (~100 K). Recently, the prospects of helium (He)-cooled MAS DNP have been increased with the instrumental developments in MAS technology that uses cold helium gas for sample cooling. Despite the additional gains in sensitivity that have been observed with He-cooled MAS DNP, the performance of the technique has not been evaluated in the case of surfaces and interfaces that benefit the most from DNP. Herein, we studied the efficiency of DNP at temperatures between ~30 K and ~100 K for organically functionalized silica material and a homogeneous solution of small organic molecules at a magnetic field B 0 = 16.4 T. We recorded the changes in signal enhancement, paramagnet-induced quenching and depolarization effects, DNP build-up rate, and Boltzmann polarization. For these samples, the increases in MAS-induced depolarization and DNP build-up times at around 30 K were not as severe as anticipated. In the case of the surface species, we determined that MAS DNP at 30 K provided ~10 times higher sensitivity than MAS DNP at 90 K, which corresponds to the acceleration of experiments by multiplicative factors of up to 100.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗